Mercurial > repos > abims-sbr > mutcount
changeset 10:f62c76aab669 draft default tip
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1
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--- a/MutCount.xml Tue Jul 03 10:55:46 2018 -0400 +++ b/MutCount.xml Mon Sep 24 04:34:39 2018 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="MutCount" id="mutcount" version="2.1.1"> +<tool name="MutCount" id="mutcount" version="2.2.0"> <description> This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests. </description> @@ -13,6 +13,7 @@ <expand macro="python_required" /> <requirement type="package" version="0.20.0">pandas</requirement> <requirement type="package" version="1.12.0">numpy</requirement> + <requirement type="package" version="1.4.4">r-optparse</requirement> </requirements> <command> @@ -20,25 +21,27 @@ ln -s $__tool_directory__/scripts/functions.py . && - #if str($method.method_run) == "concat" : + #if str($method.method_run) == "concat" : python '$__tool_directory__/scripts/S01a_codons_counting.py' ${method.concat_nuc} '$method.list_species' '$method.list_species_boot' $method.num_iter $method.num_sampled > ${log} #end if #if str($method.method_run) == "separated" : + mkdir 01_input_files && + ln -s '$__tool_directory__/scripts/S03b_sign_test_binomial.R' . && #for $input in $method.sep_file - ln -s '$input' '$input.element_identifier'; - echo '$input.element_identifier' >> list_files; + ln -s '$input' '01_input_files/$input.element_identifier'; #end for #if str($method.format_run)== "nucleic" : - python '$__tool_directory__/scripts/S02b_study_seq_composition_nuc.py' ${method.concat_phy} list_files + python '$__tool_directory__/scripts/S01b_extract_variable_nuc.py' ${method.sps_list} && #end if #if str($method.format_run)== "proteic" : - cp '$__tool_directory__/scripts/amino_acid_properties.csv' . - && - python '$__tool_directory__/scripts/S01b_study_seq_composition_aa.py' ${method.concat_phy} list_files + cp '$__tool_directory__/scripts/amino_acid_properties.csv' . && + python '$__tool_directory__/scripts/S01b_extract_variable_prot.py' ${method.sps_list} amino_acid_properties.csv && #end if + + python '$__tool_directory__/scripts/S02b_extreme_2states.py' ${method.sps_gp1} ${method.sps_gp2} ${method.format_run} #end if ]]> @@ -54,7 +57,7 @@ <when value="concat"> <param name="concat_nuc" type="data" format="fasta" label="Choose your fasta file in nucleic format" help="It must contain the concatenated file in NUCLEIC format from Phylogeny tool" /> <param name="list_species" type="text" size="100" label="List of species for countings" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" /> - <param name="list_species_boot" type="text" size="100" label="List of species used for resampling" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" /> + <param name="list_species_boot" type="text" size="100" label="List of species (at least two) used for resampling" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" /> <param name="num_iter" type="integer" value="1000" min="0" label="Number of sampled codons" help="Sets the length (in codons) of the resampled sequences"/> <param name="num_sampled" type="integer" value="1000" min="0" label="Number of iterations" help="Sets the number of resampled sequences"/> </when> @@ -64,8 +67,10 @@ <option value="nucleic">Nucleic format</option> <option value="proteic">Proteic format</option> </param> - <param name="sep_file" type="data" format="fasta" multiple="true" label="Choose fasta files" help="Concatenated files from ORF_search tool ; in nucleic or proteic, according to the format chosen above" /> - <param name="concat_phy" type="data" format="fasta" label="Concatenated file from Phylogeny step" help="This file is used to retrieve the species names" /> + <param name="sep_file" type="data" format="fasta" multiple="true" label="Choose fasta files" help="Fasta files from ORF_search tool ; in nucleic or proteic, according to the format chosen above" /> + <param name="sps_list" type="text" size="100" label="Enter all the studied species" help="Enter all the species present in the set of fasta files (comma-separated abbreviated names)" /> + <param name="sps_gp1" type="text" size="100" label="Species for group one" help="Specify species (comma-separated abbreviated names) sharing an ecological condition"/> + <param name="sps_gp2" type="text" size="100" label="Species for group two" help="Specify species (comma-separated abbreviated names) sharing an other ecological condition"/> </when> </conditional> </inputs> @@ -98,63 +103,44 @@ </data> <!-- outputs separated - nucleic --> - <data format="csv" name="nuc_comp" label="nuc_compositions.csv" from_work_dir="OUT/nuc_compositions.csv" > + <collection name="tables_nuc" type="list" label="counts_on_nucleotides"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_nucleotide" /> <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> - </data> - <data format="csv" name="percent_gc" label="percent_GC.csv" from_work_dir="OUT/percent_GC.csv" > + </collection> + <collection name="tables_nuc_var" type="list" label="counts_on_nuc_variables"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_nuc_variable" /> <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> - </data> - <data format="csv" name="percent_pur" label="percent_purine.csv" from_work_dir="OUT/percent_purine.csv" > + </collection> + <collection name="outputs_nuc" type="list" label="binomial_tests_on_nucleotides"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_nucleotides" /> <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> - </data> - <data format="csv" name="purine_load" label="Purine_Load_Indice.csv" from_work_dir="OUT/Purine_Load_Indice.csv" > + </collection> + <collection name="outputs_nuc_var" type="list" label="binomial_tests_on_nuc_variables"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_nuc_variables" /> <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> - </data> + </collection> <!-- outputs separated - proteic --> - <data format="csv" name="prot_comp" label="prot_compositions_All_AA.csv" from_work_dir="OUT/prot_compositions_All_AA.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="ivywrel" label="IVYWREL.csv" from_work_dir="OUT/IVYWREL.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="erk_dnqtsh" label="ERK_DNQTSH.csv" from_work_dir="OUT/ERK_DNQTSH.csv" > + <collection name="tables_aa" type="list" label="counts_on_amino_acids"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_aa" /> <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="ek_qh" label="EK_QH.csv" from_work_dir="OUT/EK_QH.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="fymink_garp" label="FYMINK_GARP.csv" from_work_dir="OUT/FYMINK_GARP.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="avlimfyw" label="AVLIMFYW.csv" from_work_dir="OUT/AVLIMFYW.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="stnq" label="STNQ.csv" from_work_dir="OUT/STNQ.csv" > + </collection> + <collection name="tables_variables" type="list" label="counts_on_indices"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_aa_variable" /> <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="rhkde" label="RHKDE.csv" from_work_dir="OUT/RHKDE.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="payre_mvgds" label="PAYRE-MVGDS.csv" from_work_dir="OUT/PAYRE-MVGDS.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="res_weigth" label="TotalResidueWeight.csv" from_work_dir="OUT/TotalResidueWeight.csv" > + </collection> + <collection name="outputs_aa" type="list" label="binomial_tests_on_amino_acids"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_aa" /> <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="res_vol" label="TotalResidueVolume.csv" from_work_dir="OUT/TotalResidueVolume.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="spec_vol" label="TotalPartialSpecificVolume.csv" from_work_dir="OUT/TotalPartialSpecificVolume.csv" > + </collection> + <collection name="outputs_variables" type="list" label="binomial_tests_on_indices"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_aa_variables" /> <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - <data format="csv" name="hydrat" label="TotalHydratation.csv" from_work_dir="OUT/TotalHydratation.csv" > - <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> - </data> - + </collection> </outputs> <tests> + <test> <conditional name="method" > <param name="method_run" value="concat" /> @@ -173,62 +159,168 @@ <output name="aa_transitions_freqs" value="OUT_concat/aa_transitions_freqs.csv" lines_diff="72"/> <output name="aatypes_transitions_freqs" value="OUT_concat/aatypes_transitions_freqs.csv" lines_diff="72"/> </test> + <test> <conditional name="method" > <param name="method_run" value="separated" /> <param name="format_run" value="nucleic" /> - <param name="sep_file" ftype="fasta" value="sep_nuc/orthogroup_1_sp6_sp6.fasta,sep_nuc/orthogroup_1_sp8_sp8.fasta,sep_nuc/orthogroup_2_sp6_sp6.fasta" /> - <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> + <param name="sep_file" ftype="fasta" value="sep_nuc/orthogroup_109_with_3_species.fasta,sep_nuc/orthogroup_113_with_4_species.fasta,sep_nuc/orthogroup_253_with_2_species.fasta,sep_nuc/orthogroup_283_with_2_species.fasta,sep_nuc/orthogroup_299_with_2_species.fasta,sep_nuc/orthogroup_301_with_4_species.fasta,sep_nuc/orthogroup_316_with_4_species.fasta,sep_nuc/orthogroup_335_with_4_species.fasta,sep_nuc/orthogroup_343_with_4_species.fasta,sep_nuc/orthogroup_368_with_4_species.fasta,sep_nuc/orthogroup_404_with_4_species.fasta,sep_nuc/orthogroup_442_with_4_species.fasta,sep_nuc/orthogroup_487_with_4_species.fasta,sep_nuc/orthogroup_508_with_4_species.fasta,sep_nuc/orthogroup_544_with_4_species.fasta,sep_nuc/orthogroup_546_with_4_species.fasta,sep_nuc/orthogroup_588_with_4_species.fasta,sep_nuc/orthogroup_623_with_4_species.fasta,sep_nuc/orthogroup_651_with_4_species.fasta,sep_nuc/orthogroup_660_with_4_species.fasta,sep_nuc/orthogroup_696_with_4_species.fasta,sep_nuc/orthogroup_707_with_4_species.fasta,sep_nuc/orthogroup_727_with_4_species.fasta,sep_nuc/orthogroup_761_with_4_species.fasta" /> + <param name="sps_list" value="Ha,Lf,Bs,Bj" /> + <param name="sps_gp1" value="Ha,Lf" /> + <param name="sps_gp2" value="Bs,Bj" /> </conditional> - <output name="nuc_comp"> - <assert_contents> - <has_line line="orthogroup_2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,NA,NA,NA,NA,0.30208,0.24479,0.19792,0.25521,NA,NA,NA,NA,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,NA,NA,NA,NA,NA,NA,NA,NA,0.31771,0.25521,0.17708,0.25000"/> - </assert_contents> - </output> - <output name="percent_gc"> - <assert_contents> - <has_line line="orthogroup_2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833" /> - </assert_contents> - </output> - <output name="percent_pur"> - <assert_contents> - <has_line line="orthogroup_2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083" /> - </assert_contents> - </output> - <output name="purine_load"> - <assert_contents> - <has_line line="orthogroup_2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,NA,NA,NA,NA,NA,192,11,11,57.29167,57.29167,NA,NA,NA,NA,NA,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,192,14,12,72.91667,62.50000" /> - </assert_contents> - </output> - </test> - + <output_collection name="tables_nuc" type="list" count="4"> + <element name="A" file="OUT_nuc/02_tables_per_nucleotide/A.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="C" file="OUT_nuc/02_tables_per_nucleotide/C.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="G" file="OUT_nuc/02_tables_per_nucleotide/G.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="T" file="OUT_nuc/02_tables_per_nucleotide/T.csv" ftype="csv" compare="diff" lines_diff="8" /> + </output_collection> + <output_collection name="tables_nuc_var" type="list" count="8"> + <element name="DIFF_AT" file="OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DIFF_GC" file="OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="GC_percent" file="OUT_nuc/02_tables_per_nuc_variable/_GC_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="PLI_AT" file="OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_AT_1000" file="OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC" file="OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC_1000" file="OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="purine_percent" file="OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="outputs_nuc" type="list" count="4"> + <element name="A" file="OUT_nuc/04_outputs_nucleotides/A.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="C" file="OUT_nuc/04_outputs_nucleotides/C.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="G" file="OUT_nuc/04_outputs_nucleotides/G.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="T" file="OUT_nuc/04_outputs_nucleotides/T.csv" ftype="csv" compare="diff" lines_diff="8" /> + </output_collection> + <output_collection name="outputs_nuc_var" type="list" count="8"> + <element name="DIFF_AT" file="OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DIFF_GC" file="OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="GC_percent" file="OUT_nuc/04_outputs_nuc_variables/GC_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="PLI_AT" file="OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_AT_1000" file="OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC" file="OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC_1000" file="OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="purine_percent" file="OUT_nuc/04_outputs_nuc_variables/purine_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + </test> + <test> <conditional name="method" > <param name="method_run" value="separated" /> <param name="format_run" value="proteic" /> - <param name="sep_file" ftype="fasta" value="sep_aa/orthogroup_1_sp6_sp6.fasta,sep_aa/orthogroup_1_sp8_sp8.fasta,sep_aa/orthogroup_2_sp6_sp6.fasta" /> - <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> - </conditional> - <output name="ivywrel"> - <assert_contents> - <has_line line="orthogroup_1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065" /> - </assert_contents> - </output> - <output name="rhkde"> - <assert_contents> - <has_line line="orthogroup_1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949"/> - </assert_contents> - </output> - <output name="payre_mvgds"> - <assert_contents> - <has_line line="orthogroup_1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750"/> - </assert_contents> - </output> - <output name="avlimfyw"> - <assert_contents> - <has_line line="orthogroup_2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375"/> - </assert_contents> - </output> + <param name="sep_file" ftype="fasta" value="sep_aa/locus_3sp_2.fasta,sep_aa/locus_3sp_7.fasta,sep_aa/locus_4sp_4.fasta,sep_aa/locus_4sp_6.fasta,sep_aa/locus_6sp_10.fasta,sep_aa/locus_6sp_11.fasta,sep_aa/locus_6sp_16.fasta,sep_aa/locus_6sp_18.fasta,sep_aa/locus_6sp_25.fasta,sep_aa/locus_6sp_27.fasta,sep_aa/locus_6sp_30.fasta,sep_aa/locus_6sp_32.fasta,sep_aa/locus_6sp_35.fasta,sep_aa/locus_6sp_38.fasta,sep_aa/locus_6sp_39.fasta,sep_aa/locus_6sp_40.fasta,sep_aa/locus_6sp_41.fasta,sep_aa/locus_6sp_46.fasta,sep_aa/locus_6sp_47.fasta,sep_aa/locus_6sp_50.fasta,sep_aa/locus_6sp_53.fasta,sep_aa/locus_6sp_57.fasta,sep_aa/locus_6sp_58.fasta,sep_aa/locus_6sp_60.fasta" /> + <param name="sps_list" value="Ps,Pp,Pf,Ac,Pg,Ap" /> + <param name="sps_gp1" value="Pp,Pg" /> + <param name="sps_gp2" value="Ap,Ps" /> + </conditional> + <output_collection name="tables_aa" type="list" count="20"> + <element name="A" file="OUT_aa/02_tables_per_aa/A.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="C" file="OUT_aa/02_tables_per_aa/C.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="D" file="OUT_aa/02_tables_per_aa/D.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="E" file="OUT_aa/02_tables_per_aa/E.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="F" file="OUT_aa/02_tables_per_aa/F.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="G" file="OUT_aa/02_tables_per_aa/G.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="H" file="OUT_aa/02_tables_per_aa/H.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="I" file="OUT_aa/02_tables_per_aa/I.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="K" file="OUT_aa/02_tables_per_aa/K.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="L" file="OUT_aa/02_tables_per_aa/L.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="M" file="OUT_aa/02_tables_per_aa/M.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="N" file="OUT_aa/02_tables_per_aa/N.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="P" file="OUT_aa/02_tables_per_aa/P.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Q" file="OUT_aa/02_tables_per_aa/Q.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="R" file="OUT_aa/02_tables_per_aa/R.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="S" file="OUT_aa/02_tables_per_aa/S.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="T" file="OUT_aa/02_tables_per_aa/T.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="V" file="OUT_aa/02_tables_per_aa/V.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="W" file="OUT_aa/02_tables_per_aa/W.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Y" file="OUT_aa/02_tables_per_aa/Y.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="tables_variables" type="list" count="26"> + + <element name="AC" file="OUT_aa/02_tables_per_aa_variable/AC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="APGC" file="OUT_aa/02_tables_per_aa_variable/APGC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIM" file="OUT_aa/02_tables_per_aa_variable/AVLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIMFYW" file="OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DE" file="OUT_aa/02_tables_per_aa_variable/DE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DNQTSHA" file="OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="EK" file="OUT_aa/02_tables_per_aa_variable/EK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ERK" file="OUT_aa/02_tables_per_aa_variable/ERK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYMINK" file="OUT_aa/02_tables_per_aa_variable/FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYW" file="OUT_aa/02_tables_per_aa_variable/FYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="GARP" file="OUT_aa/02_tables_per_aa_variable/GARP.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="IVYWREL" file="OUT_aa/02_tables_per_aa_variable/IVYWREL.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="QH" file="OUT_aa/02_tables_per_aa_variable/QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_AC_VLIM" file="OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_APGC_VLIM" file="OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_EK_QH" file="OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_ERK_DNQTSHA" file="OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_GARP_FYMINK" file="OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHK" file="OUT_aa/02_tables_per_aa_variable/RHK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHKDE" file="OUT_aa/02_tables_per_aa_variable/RHKDE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="STNQ" file="OUT_aa/02_tables_per_aa_variable/STNQ.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="total_hydratation" file="OUT_aa/02_tables_per_aa_variable/total_hydratation.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="total_partial_specific_volume" file="OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_volume" file="OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_weight" file="OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="VLIM" file="OUT_aa/02_tables_per_aa_variable/VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="outputs_aa" type="list" count="20"> + <element name="A" file="OUT_aa/04_outputs_aa/A.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="C" file="OUT_aa/04_outputs_aa/C.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="D" file="OUT_aa/04_outputs_aa/D.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="E" file="OUT_aa/04_outputs_aa/E.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="F" file="OUT_aa/04_outputs_aa/F.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="G" file="OUT_aa/04_outputs_aa/G.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="H" file="OUT_aa/04_outputs_aa/H.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="I" file="OUT_aa/04_outputs_aa/I.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="K" file="OUT_aa/04_outputs_aa/K.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="L" file="OUT_aa/04_outputs_aa/L.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="M" file="OUT_aa/04_outputs_aa/M.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="N" file="OUT_aa/04_outputs_aa/N.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="P" file="OUT_aa/04_outputs_aa/P.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Q" file="OUT_aa/04_outputs_aa/Q.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="R" file="OUT_aa/04_outputs_aa/R.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="S" file="OUT_aa/04_outputs_aa/S.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="T" file="OUT_aa/04_outputs_aa/T.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="V" file="OUT_aa/04_outputs_aa/V.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="W" file="OUT_aa/04_outputs_aa/W.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Y" file="OUT_aa/04_outputs_aa/Y.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="outputs_variables" type="list" count="26"> + <element name="AC" file="OUT_aa/04_outputs_aa_variables/AC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="APGC" file="OUT_aa/04_outputs_aa_variables/APGC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIM" file="OUT_aa/04_outputs_aa_variables/AVLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIMFYW" file="OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DE" file="OUT_aa/04_outputs_aa_variables/DE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DNQTSHA" file="OUT_aa/04_outputs_aa_variables/DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="EK" file="OUT_aa/04_outputs_aa_variables/EK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ERK" file="OUT_aa/04_outputs_aa_variables/ERK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYMINK" file="OUT_aa/04_outputs_aa_variables/FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYW" file="OUT_aa/04_outputs_aa_variables/FYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="GARP" file="OUT_aa/04_outputs_aa_variables/GARP.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="IVYWREL" file="OUT_aa/04_outputs_aa_variables/IVYWREL.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="QH" file="OUT_aa/04_outputs_aa_variables/QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_AC_VLIM" file="OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_APGC_VLIM" file="OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_EK_QH" file="OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_ERK_DNQTSHA" file="OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_GARP_FYMINK" file="OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHK" file="OUT_aa/04_outputs_aa_variables/RHK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHKDE" file="OUT_aa/04_outputs_aa_variables/RHKDE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="STNQ" file="OUT_aa/04_outputs_aa_variables/STNQ.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="total_hydratation" file="OUT_aa/04_outputs_aa_variables/total_hydratation.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="total_partial_specific_volume" file="OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_volume" file="OUT_aa/04_outputs_aa_variables/total_residue_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_weight" file="OUT_aa/04_outputs_aa_variables/total_residue_weight.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="VLIM" file="OUT_aa/04_outputs_aa_variables/VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> </test> </tests> @@ -239,18 +331,25 @@ <![CDATA[ -**Last Version** : Victor Mataigne and Gildas Le Corguillé - --------- - **Description** -This script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences. Counting is then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences. +*1-Separated mode* + +Input files are all the orthogroups computed by the AdaptSearch suite; Counts and test are computed on each group separatly. This mode counts occurrences of amino-acids or nucleic acids, according to the sequences type, in each distinct orthogroup. Then, two subgroups of species are set by the user : + +- A first group, constitued by species having something in common (an ecological trait, an ecological niche, a particular environmental adaptation) +- A second group, constitued by species sharing the opposite trait (for example, the user can have a first subgroup made with species adapted to high temperatures and a second group made with species adapted to cold temperatures) + +Within the groups, the program checks wether the occurrences of each element (amino-acid, nucleic acid, thermostability indice, GC content …) is higher of lower between one species and all the species of the opposite group. Binomial tests are then performed of these counts. + +*2-Concatenated mode* + +The input file is the super-alignment obtained by concatenation of all the orthogroups computed by the AdaptSearch suite. This script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences. Counts are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences. -In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting. +In the output files, the pvalues indicate the position of the observed data in a distribution of empirical counts obtained from a resampling of the data. Values above 0.95 indicate a significantly higher count, values under 0.05 a significantly lower count. -The script resamples random pairs of aligned codon to determine what countings can be expected under the hypothesis of an homogenous dataset. -Countings are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the countings. +The script resamples random pairs of aligned codon to determine what counts can be expected under the hypothesis of an homogenous dataset. +Counts are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the counts. Then the script simply checks whether the observed data are within the 5% lowest or 5% highest values of the distribution. -------- @@ -273,11 +372,11 @@ - The list of species for **countings**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species, not only on the total number of species present in the previous tools. -- The list of species for **resampling**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species, not only on the total number of species present in the previous tools. +- The list of species for **resampling**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species (at least two species), not only on the total number of species present in the previous tools. - The number of iterations : the number of alignments that will be generated (effect on the resolution of the gaussian distribution). Shouldn't be lower than 1000 to have a relatively smooth gaussian distribution. -- The number of sampled codons : the number of pairs of codons in each generated alignments (effect on the robustness on the countings performed on this alignement). Shouldn't be lower than 1000 to detect codons with relatively low occurence (<1%). +- The number of sampled codons : the number of pairs of codons in each generated alignments (effect on the robustness on the counts performed on this alignement). Shouldn't be lower than 1000 to detect codons with relatively low occurence (<1%). -------- @@ -285,9 +384,8 @@ Many outputs in .csv format , varying according to the chosen method and format (separated, nucleic ...) - When method = concat : 6 .csv outputs : countings of codons, amino acids, amino acids types, and transitions from amino acid to amino acid and from amino acid type to amino acid type. - - When method = separated and format = nucleic : 4 .csv outputs : nucleotide composition, GC percent, purine percent, purine load indice. - - When method = separated and format = proteic : 13 .csv outputs : protein composition, several files of countings various AA combinations, results on residues, hydratation, partial specific volume. - + - When method = separated and format = nucleic : 4 collections with several .csv files : counts tables and binomial sign tests results for nucleotides and various indices (GC and purine percent ...) . + - When method = separated and format = proteic : 4 collections with several .csv files : counts tables and binomial sign tests results for amino-acids and various indices (thermophilic indices, hydratation, partial specific volume...). --------- **The AdaptSearch Pipeline** @@ -299,6 +397,9 @@ Changelog --------- +**Version 2.2.0 - 10/07/2018** +- Updated separated mode : added a binomial sign test + **Version 2.1 - 26/02/2017** - Fully re-written the concat method : fixed mistakes + cleaner code - Splitted output of concatenated method in several csv files. @@ -319,7 +420,5 @@ ]]> </help> - - <expand macro="citations" /> </tool>
--- a/macros.xml Tue Jul 03 10:55:46 2018 -0400 +++ b/macros.xml Mon Sep 24 04:34:39 2018 -0400 @@ -7,13 +7,14 @@ <token name="@HELP_AUTHORS@"> .. class:: infomark -**Authors** Eric Fontanillas creates the scripts of this pipeline. +**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2. .. class:: infomark -**Galaxy integration** ABiMS TEAM +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor ---------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01b_extract_variable_nuc.py Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,121 @@ +#!/usr/bin/env python +#coding: utf-8 + +import argparse, os +from functions import dico, write_output, fill_with_NaN + +""" Functions for nucleic format """ + +def all_nuc_counts(seq): + """ Counts the number of nucleotides in a sequence + + Args : + - seq (String) : a nucleic sequence + + Return: + - nuc_counts (dict) : counts on nucleotides (key/value : nucleotide/count) + """ + nuc_counts = {} + seqU = seq.upper() + LN =['A','C','T','G'] + + for base in LN: + nuc_counts[base] = seqU.count(base) + + return nuc_counts + +def ratios(nuc_counts): + """ Compute GC and purine ratios from the counts of nucleotides in a sequence + + Args : + - nuc_counts (dict) : dictionary of nucleotides counts (output of all_nuc_counts()) + + Return : + - ratios (dict) : dictionary with ratios + """ + + # Search for compositional bias in genome as marker of thermal adaptation + ratios = {} + ratios['GC_percent'] = float(nuc_counts['C'] + nuc_counts['G'])/(sum(nuc_counts.values())*100) + ratios['purine_percent'] = float(nuc_counts['A'] + nuc_counts['G'])/(sum(nuc_counts.values())*100) + + ratios['DIFF_GC'] = nuc_counts['G'] - nuc_counts['C'] + ratios['DIFF_AT'] = nuc_counts['A'] - nuc_counts['T'] + + # Per bp + ratios['PLI_GC'] = float(ratios['DIFF_GC'])/sum(nuc_counts.values()) + ratios['PLI_AT'] = float(ratios['DIFF_AT'])/sum(nuc_counts.values()) + + # Per 1000 bp + ratios['PLI_GC_1000'] = ratios['PLI_GC']*1000 + ratios['PLI_AT_1000'] = ratios['PLI_AT']*1000 + + return ratios + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("species_list", help="List of species separated by commas") + args = parser.parse_args() + + LN =['A','C','T','G'] + Lratios = ['GC_percent', 'purine_percent', 'DIFF_GC', 'DIFF_AT', 'PLI_GC', 'PLI_AT', 'PLI_GC_1000', 'PLI_AT_1000'] + + list_inputs = [] + + path_inputs = '01_input_files' + list_inputs = os.listdir(path_inputs) + + lsp = args.species_list.split(',') + lsp = sorted(lsp) + flsp = '' + for el in lsp: + flsp += el+',' + + path_outputs_1 = '02_tables_per_nucleotide' + path_outputs_2 = '02_tables_per_nuc_variable' + os.mkdir(path_outputs_1) + os.mkdir(path_outputs_2) + + dict_for_files_nuc = {} + dict_for_file_var = {} + + # All counts + for file in list_inputs: + # iterate over input files + sequences = dico(file, path_inputs) + + # TEMPORARY CORRECTION FOR SEQUENCES CONTAINING ONLY INDELS + # It appears than CDS_Search can bug sometimes and return an alignement where a species' sequence is made of indels only + # This causes a crash here (in the ratios function). The correction skip the whole file. + # When CDS_Search is corrected, lines with 'skip' can be removed + skip = False + for key in sequences.keys(): + if all(x == '-' for x in sequences[key]): + skip = True + + if not skip: + + nuc_counts_per_seq = {} + nuc_var_per_seq = {} + + for key in sequences.keys(): + # iterate over sequences in the file + nuc_counts_per_seq[key] = all_nuc_counts(sequences[key]) + nuc_var_per_seq[key] = ratios(nuc_counts_per_seq[key]) + + # Add NaN for missing species + for key in set(lsp).difference(set(sequences.keys())): + nuc_counts_per_seq[key] = fill_with_NaN(LN) + nuc_var_per_seq[key] = fill_with_NaN(Lratios) + + # Add computations to final dicts + dict_for_files_nuc[file] = nuc_counts_per_seq + dict_for_file_var[file] = nuc_var_per_seq + + + # Try with pandas ? + write_output(LN, flsp, path_outputs_1, dict_for_files_nuc) # one file per nuc + write_output(Lratios, flsp, path_outputs_2, dict_for_file_var) # one file per nuc_variable + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01b_extract_variable_prot.py Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,321 @@ +#!/usr/bin/env python +#coding: utf-8 +#Author : Eric Fontanillas (2010) - Victor Mataigne (2018) + +# TODO : + # - Deal with missing data : do not do the sign test if missing species in a group + # - Find a way to avoid the list_species argument + +import argparse, os +from functions import dico, write_output, fill_with_NaN + +def aa_properties(amino_acids_properties_file): + """ Read the file 'amino_acids_properties' and stores its content + + Args : + amino_acids_properties_file (String) : the file + + Return : + aa_properties (dict) : key/amino-acid - value/list of properties + """ + + dict_aa_properties={} + with open(amino_acids_properties_file, 'r') as f: + f.readline() #jump headers + for line in f.readlines(): + S1 = line.split(",") + aa_name = S1[1] + S2 = aa_name.split("/") + aa_code = S2[1][:-1] + + frequencies = S1[2][:-1] + residue_weight = S1[5] + residue_volume = S1[6] + partial_specific_volume = S1[7] + hydration = S1[8] + + dict_aa_properties[aa_code] = [frequencies, residue_weight, residue_volume, partial_specific_volume, hydration] + + return(dict_aa_properties) + +""" Functions for proteic format """ + +def all_aa_counts(seq): + """ Count the occurrences of all amino-acids in a sequence + + Args: + seq (String) : a proteic sequence + + Returns: a dictionary with amino-acids counts + """ + + aa_counts = {} + seqU = seq.upper() + LAA =['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G'] + + for aa in LAA: + aa_counts[aa] = seqU.count(aa) + + return aa_counts + +def all_aa_props(seq_counts): + """ Converts a dictionnary of counts into a dictionnary of proportions + + Args: + seq_counts (dict) : dictionnary computed by the function all_aa_counts() + + Returns: a dictionary with counts replaced by proportions + """ + + aa_props = {} + for key in seq_counts.keys(): + aa_props[key] = float(seq_counts[key]) / sum(seq_counts.values()) + return aa_props + +def aa_variables_counts_and_props(aa_counts): + """ Computes several thermostability indices (summed occurrences of some AAs, and then various ratios) + + Args: + aa_counts (dict) : dictionnary computed by the function all_aa_counts() + + Returns: + aa_variables_counts : a dictionary with indices values + aa_variables_props : a dictionary with indices proportions (ratios excluded) + """ + + # Hyperthermophile Prokaryotes criterias + # IVYWREL : positivelly correlated with otpimal growth + # ERK : (i.e. ) => positivelly correlated with optimal growth temperature + # ERK/DNQTSHA (or DNQTSH ??) + # EK/QH + + # Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP + # The mutational bias model predict a linear relationship between GARP vs FYMINK + # ==> so if outliers to that, it means that the excess of GARP or FYMINK are not explained by the mutationnal bias model but by something else (selection ?) + + + # Hydophobicity hypothesis [should INCREASE with thermal adaptation] + # AL + # Only non-aromatic : AVLIM + # Only aromatic : FYW + + # Charged hypothesis => positivelly correlated with optimal growth temperature + # All charged : RHKDE + # Only positive : RHK + # Only negative : DE + + # Neutral polar hypothesis [should DECREASE with thermal adaptation] + # STNQ + + # Fontanillas' criteria + # PAYRE + # MVGDS + # PAYRE/MVGDS + + # Jollivet's criteria + # AC + # MVGDS + # AC/MVGDS + + aa_variables_counts = {} + aa_variables_props = {} + len_seq = sum(aa_counts.values()) # length of the sequence + + # counts of variables + aa_variables_counts['AC'] = aa_counts['A'] + aa_counts['C'] + aa_variables_counts['APGC'] = aa_counts['A'] + aa_counts['P'] + aa_counts['G'] + aa_counts['C'] + aa_variables_counts['AVLIM'] = aa_counts['A'] + aa_counts['V'] + aa_counts['L'] + aa_counts['I'] + aa_counts['M'] + aa_variables_counts['AVLIMFYW'] = aa_variables_counts['AVLIM'] + aa_counts['F'] + aa_counts['Y'] + aa_counts['W'] + aa_variables_counts['DE'] = aa_counts['D'] + aa_counts['E'] + aa_variables_counts['DNQTSHA'] = aa_counts['D'] + aa_counts['N'] + aa_counts['Q'] + aa_counts['T'] + aa_counts['S'] + aa_counts['H'] + aa_counts['A'] + aa_variables_counts['EK'] = aa_counts['E'] + aa_counts['K'] + aa_variables_counts['ERK'] = aa_counts['E'] + aa_counts['K'] + aa_counts['K'] + aa_variables_counts['FYMINK'] = aa_counts['F'] + aa_counts['Y'] + aa_counts['M'] + aa_counts['I'] + aa_counts['N'] + aa_counts['K'] + aa_variables_counts['FYW'] = aa_counts['F'] + aa_counts['Y'] + aa_counts['W'] + aa_variables_counts['GARP'] = aa_counts['G'] + aa_counts['A'] + aa_counts['R'] + aa_counts['P'] + aa_variables_counts['IVYWREL'] = aa_counts['I'] + aa_counts['V'] + aa_counts['Y'] + aa_counts['W'] + aa_counts['R'] + aa_counts['E'] + aa_counts['L'] + aa_variables_counts['QH'] = aa_counts['Q'] + aa_counts['H'] + aa_variables_counts['RHK'] = aa_counts['R'] + aa_counts['H'] + aa_counts['K'] + aa_variables_counts['RHKDE'] = aa_counts['R'] + aa_counts['H'] + aa_counts['K'] + aa_counts['D'] + aa_counts['E'] + aa_variables_counts['STNQ'] = aa_counts['S'] + aa_counts['T'] + aa_counts['N'] + aa_counts['Q'] + aa_variables_counts['VLIM'] = aa_counts['V'] + aa_counts['L'] + aa_counts['I'] + aa_counts['M'] + aa_variables_counts['PAYRE'] = aa_counts['P'] + aa_counts['A'] + aa_counts['Y'] + aa_counts['R'] + aa_counts['E'] + aa_variables_counts['MVGDS'] = aa_counts['M'] + aa_counts['V'] + aa_counts['G'] + aa_counts['D'] + aa_counts['S'] + + # compute proportions + for key in aa_variables_counts.keys(): + aa_variables_props[key] = float(aa_variables_counts[key]) / float(len_seq) + + if aa_variables_counts['DNQTSHA'] != 0: + ratio_ERK_DNQTSHA = float(aa_variables_counts['ERK'])/float(aa_variables_counts['DNQTSHA']) + else : + ratio_ERK_DNQTSHA = -1 + + if aa_variables_counts['QH'] != 0: + ratio_EK_QH = float(aa_variables_counts['EK'])/float(aa_variables_counts['QH']) + else : + ratio_EK_QH = -1 + + if aa_variables_counts['FYMINK'] != 0: + ratio_GARP_FYMINK = float(aa_variables_counts['EK'])/float(aa_variables_counts['FYMINK']) + else : + ratio_GARP_FYMINK = -1 + + if aa_variables_counts['VLIM'] != 0: + ratio_AC_VLIM = float(aa_variables_counts['AC'])/float(aa_variables_counts['VLIM']) + ratio_APGC_VLIM = float(aa_variables_counts['APGC'])/float(aa_variables_counts['VLIM']) + else : + ratio_AC_VLIM = -1 + ratio_APGC_VLIM = -1 + + if aa_variables_counts['MVGDS'] != 0: + ratio_PAYRE_MVGDS = float(aa_variables_counts['PAYRE'])/float(aa_variables_counts['MVGDS']) + else : + ratio_PAYRE_MVGDS = -1 + + if aa_variables_counts['MVGDS'] != 0: + ratio_AC_MVGDS = float(aa_variables_counts['AC'])/float(aa_variables_counts['MVGDS']) + else : + ratio_AC_MVGDS = -1 + + aa_variables_counts['ratio_ERK_DNQTSHA'] = ratio_ERK_DNQTSHA + aa_variables_counts['ratio_EK_QH'] = ratio_EK_QH + aa_variables_counts['ratio_GARP_FYMINK'] = ratio_GARP_FYMINK + aa_variables_counts['ratio_AC_VLIM'] = ratio_AC_VLIM + aa_variables_counts['ratio_APGC_VLIM'] = ratio_APGC_VLIM + aa_variables_counts['ratio_PAYRE_MVGDS'] = ratio_PAYRE_MVGDS + aa_variables_counts['ratio_AC_MVGDS'] = ratio_AC_MVGDS + + return aa_variables_counts, aa_variables_props + +def sequence_properties_from_aa_properties(aa_counts, aa_properties): + """ Computes a sequence properties (based on an external data file) + + Args: + - aa_counts (dict) : counts of amino-acids in the sequence + - aa_properties (dict) : key/amino-acid - value/list of properties extract from the external data file + + Returns: + - seq_props (dict) : values of the sequence properties + """ + + LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation'] + seq_props = {} + + for i in range(1,5): + seq_props[LS[i-1]] = 0 + for key in aa_counts.keys(): + seq_props[LS[i-1]] += aa_counts[key] * float(aa_properties[key][i]) + + return seq_props + +""" Main """ + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("species_list", help="List of species separated by commas") + parser.add_argument("aa_properties", help="File with all amino-acids properties") + args = parser.parse_args() + + LAA = ['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G'] + LV = ['IVYWREL','EK','ERK','DNQTSHA','QH','ratio_ERK_DNQTSHA','ratio_EK_QH','FYMINK','GARP', + 'ratio_GARP_FYMINK','AVLIM','FYW','AVLIMFYW','STNQ','RHK','DE','RHKDE','APGC','AC', + 'VLIM','ratio_AC_VLIM','ratio_APGC_VLIM'] + LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation'] + + list_inputs = [] + + path_inputs = '01_input_files' + list_inputs = os.listdir(path_inputs) + + lsp = args.species_list.split(',') + lsp = sorted(lsp) + flsp = '' + for el in lsp: + flsp += el+',' + + path_outputs_1 = '02_tables_per_aa' + path_outputs_2 = '02_tables_per_aa_variable' + os.mkdir(path_outputs_1) + os.mkdir(path_outputs_2) + + # Init empty dicts for results + dict_for_files_aa_counts = {} # counts + dict_for_files_aa_props = {} # proportions + dict_for_files_variables_counts = {} + dict_for_files_variables_props = {} + dict_for_files_seq_properties = {} + + aa_properties_file = aa_properties(args.aa_properties) # read the aa_properties file + + # All counts and props + for file in list_inputs: + # iterate over input files + sequences = dico(file, path_inputs) + + # TEMPORARY CORRECTION FOR SEQUENCES CONTAINING ONLY INDELS + # It appears than CDS_Search can bug sometimes and return an alignement where a species' sequence is made of indels only + # This causes a crash here (in the ratios function). The correction skip the whole file. + # When CDS_Search is corrected, lines with 'skip' can be removed + skip = False + for key in sequences.keys(): + if all(x == '-' for x in sequences[key]): + skip = True + + if not skip: + + aa_counts_per_seq = {} + aa_props_per_seq = {} + aa_variables_counts_per_seq = {} + aa_variables_props_per_seq = {} + seq_properties = {} + + for key in sequences.keys(): + # iterate over sequences in the file + aa_counts_per_seq[key] = all_aa_counts(sequences[key]) + aa_props_per_seq[key] = all_aa_props(aa_counts_per_seq[key]) + aa_variables_counts_per_seq[key], aa_variables_props_per_seq[key] = aa_variables_counts_and_props(aa_counts_per_seq[key]) + seq_properties[key] = sequence_properties_from_aa_properties(aa_counts_per_seq[key], aa_properties_file) + + # Add NaN for missing species + for key in set(lsp).difference(set(sequences.keys())): + aa_counts_per_seq[key] = fill_with_NaN(LAA) + aa_props_per_seq[key] = fill_with_NaN(LAA) + aa_variables_counts_per_seq[key] = fill_with_NaN(LV) + seq_properties[key] = fill_with_NaN(LS) + + # Add computations to final dicts + dict_for_files_aa_counts[file] = aa_counts_per_seq + dict_for_files_aa_props[file] = aa_props_per_seq + dict_for_files_variables_counts[file] = aa_variables_counts_per_seq + dict_for_files_variables_props[file] = aa_variables_props_per_seq + dict_for_files_seq_properties[file] = seq_properties + + # Try with pandas ? + write_output(LAA, flsp, path_outputs_1, dict_for_files_aa_counts) # one file per AA + write_output(LV, flsp, path_outputs_2, dict_for_files_variables_counts) # one file per aa_variable + write_output(LS, flsp, path_outputs_2, dict_for_files_seq_properties) #one file per seq properties + + # { file_name1 : { seq1: {'A' : 0, 'C':0, 'E':0, ...}, + # seq2: {'A' : 0, 'C':0, 'E':0, ...}, ... + # }, + # { file_name2 : { seq1: {'A' : 0, 'C':0, 'E':0, ...}, + # seq2: {'A' : 0, 'C':0, 'E':0, ...}, + # }, + # ... } + + # { file_name1 : {seq1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # seq2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, ... + # }, + # file_name2 : {seq1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # seq2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # }, + # ... } + + # { file_name1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # file_name2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # ... + # } + +if __name__ == '__main__': + main()
--- a/scripts/S01b_study_seq_composition_aa.py Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,622 +0,0 @@ -#!/usr/bin/env python -# -*- coding: ascii -*- -## Author: Eric FONTANILLAS -## Date: 21.12.10 -## Last Version : 12/2017 by Victor Mataigne -## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and two "cold" species: Pg, Pp) - -import sys,os,shutil,subprocess,string, itertools -from functions import simplify_fasta_name, dico - -script_path = os.path.dirname(sys.argv[0]) - -################## -###### DEF2 ###### -################## -def base_composition(seq): - count_A=string.count(seq, "A") - count_T=string.count(seq, "T") - count_C=string.count(seq, "C") - count_G=string.count(seq, "G") - - - CG = count_C+count_G - AT = count_T+count_A - - AG = count_A+count_G - TC = count_T+count_C - - ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT - ratio_CG_AT=float(CG)/float(AT) - - ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC - ratio_purine_pyrimidine=float(AG)/float(TC) - - ## 3 ## Nucleotide proportion - ln = len(seq) - prop_A = float(count_A)/float(ln) - prop_T = float(count_T)/float(ln) - prop_C = float(count_C)/float(ln) - prop_G = float(count_G)/float(ln) - - - return(ratio_CG_AT, ratio_purine_pyrimidine, prop_A, prop_T, prop_C, prop_G) -############################################## - - -################## -###### DEF3 ###### -################## -def aa_composition1(seq): - - ## 1 ## count occurence of AA - count_K=string.count(seq,"K") - count_R=string.count(seq,"R") - count_A=string.count(seq,"A") - count_F=string.count(seq,"F") - count_I=string.count(seq,"I") - count_L=string.count(seq,"L") - count_M=string.count(seq,"M") - count_V=string.count(seq,"V") - count_W=string.count(seq,"W") - count_N=string.count(seq,"N") - count_Q=string.count(seq,"Q") - count_S=string.count(seq,"S") - count_T=string.count(seq,"T") - count_H=string.count(seq,"H") - count_Y=string.count(seq,"Y") - count_C=string.count(seq,"C") - count_D=string.count(seq,"D") - count_E=string.count(seq,"E") - count_P=string.count(seq,"P") - count_G=string.count(seq,"G") - - - - ## 2 ## compute relative proportion - TOTAL=count_K+count_R+count_A+count_F+count_I+count_L+count_M+count_V+count_W+count_N+count_Q+count_S+count_T+count_H+count_Y+count_C+count_D+count_E+count_P+count_G - if (TOTAL!=0): - ln = TOTAL - - prop_K=float(count_K)/float(ln) - prop_R=float(count_R)/float(ln) - prop_A=float(count_A)/float(ln) - prop_F=float(count_F)/float(ln) - prop_I=float(count_I)/float(ln) - prop_L=float(count_L)/float(ln) - prop_M=float(count_M)/float(ln) - prop_V=float(count_V)/float(ln) - prop_W=float(count_W)/float(ln) - prop_N=float(count_N)/float(ln) - prop_Q=float(count_Q)/float(ln) - prop_S=float(count_S)/float(ln) - prop_T=float(count_T)/float(ln) - prop_H=float(count_H)/float(ln) - prop_Y=float(count_Y)/float(ln) - prop_C=float(count_C)/float(ln) - prop_D=float(count_D)/float(ln) - prop_E=float(count_E)/float(ln) - prop_P=float(count_P)/float(ln) - prop_G=float(count_G)/float(ln) - else: - prop_K=0 - prop_R=0 - prop_A=0 - prop_F=0 - prop_I=0 - prop_L=0 - prop_M=0 - prop_V=0 - prop_W=0 - prop_N=0 - prop_Q=0 - prop_S=0 - prop_T=0 - prop_H=0 - prop_Y=0 - prop_C=0 - prop_D=0 - prop_E=0 - prop_P=0 - prop_G=0 - - - - - return(prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G) - -################## -###### DEF4 ###### -################## -def aa_composition2(seq): - - ## 1 ## count occurence of AA - count_K=string.count(seq,"K") - count_R=string.count(seq,"R") - count_A=string.count(seq,"A") - count_F=string.count(seq,"F") - count_I=string.count(seq,"I") - count_L=string.count(seq,"L") - count_M=string.count(seq,"M") - count_V=string.count(seq,"V") - count_W=string.count(seq,"W") - count_N=string.count(seq,"N") - count_Q=string.count(seq,"Q") - count_S=string.count(seq,"S") - count_T=string.count(seq,"T") - count_H=string.count(seq,"H") - count_Y=string.count(seq,"Y") - count_C=string.count(seq,"C") - count_D=string.count(seq,"D") - count_E=string.count(seq,"E") - count_P=string.count(seq,"P") - count_G=string.count(seq,"G") - - - - ## 2 ## compute seq length - TOTAL=count_K+count_R+count_A+count_F+count_I+count_L+count_M+count_V+count_W+count_N+count_Q+count_S+count_T+count_H+count_Y+count_C+count_D+count_E+count_P+count_G - if (TOTAL!=0): - - ln = TOTAL - ##3 Famous Hyperthermophile Prokaryotes criterias - - # 3.1. IVYWREL estimator => positivelly correlated with otpimal growth - count_IVYWREL = count_I+count_V+count_Y+count_W+count_R+count_E+count_L - prop_IVYWREL = float(count_IVYWREL)/float(ln) - - # 3.2. ERK estimator (i.e. ERK vs DNQTSHA) => positivelly correlated with optimal growth temperature - # ERK alone - count_ERK = count_E + count_R + count_K - prop_ERK = float(count_ERK)/float(ln) - # DNQTSHA alone - count_DNQTSH = count_D+count_N+count_Q+count_T+count_S+count_H - prop_DNQTSH=float(count_DNQTSH)/float(ln) - # ERK vs DNQTSH - if count_DNQTSH != 0: - ratio_ERK_vs_DNQTSH = float(count_ERK)/float(count_DNQTSH) - else: - ratio_ERK_vs_DNQTSH=-1 - # EK/QH estimator - count_EK = count_E+count_K - count_QH = count_Q+count_H - - prop_EK = float(count_EK)/float(ln) - prop_QH = float(count_QH)/float(ln) - - if count_QH != 0: - ratio_EK_vs_QH = float(count_EK)/float(count_QH) - else: - ratio_EK_vs_QH=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator) - - ## 4 ## Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP - ## The mutational bias model predict a linear relationship between GARP vs FYMINK ==> so if outliers to that, it means that the excess of GARP or FYMINK are not explained by the mutationnal bias model but by other thing ... selection!!??? - count_FYMINK=count_F+count_Y+count_M+count_I+count_N+count_K - prop_FYMINK = float(count_FYMINK)/float(ln) - - count_GARP=count_G+count_A+count_R+count_P - prop_GARP=float(count_GARP)/float(ln) - - ## 5 ## Hydophobicity hypothesis [should INCREASE with thermal adaptation] - ## 5.1. AL - count_AVLIMFYW = count_A+count_V+count_L+count_I+count_F+count_Y+count_W+count_M - prop_AVLIMFYW=float(count_AVLIMFYW)/float(ln) - ## 5.2. Only non-aromatic - count_AVLIM = count_A+count_V+count_L+count_I+count_M - prop_AVLIM=float(count_AVLIM)/float(ln) - ## 5.3. Only aromatic (have they higher residus volume?? in such case opposite hypothesis based on residu volume, predict DECREASE for these aa in composition) - count_FYW = count_F+count_Y+count_W - prop_FYW=float(count_FYW)/float(ln) - - ## 6 ## Charged hypothesis => positivelly correlated with optimal growth temperature - # All charged - count_RHKDE = count_R + count_H +count_K + count_D + count_E - prop_RHKDE = float(count_RHKDE)/float(ln) - # Only positive - count_RHK = count_R + count_H +count_K - prop_RHK = float(count_RHK)/float(ln) - # Only negative - count_DE = count_D + count_E - prop_DE = float(count_DE)/float(ln) - - ## 7 ## Neutral polar hypothesis [should DECREASE with thermal adaptation] - count_STNQ = count_S+count_T+count_N+count_Q - prop_STNQ=float(count_STNQ)/float(ln) - - - ## 9 ## PAYRE VS MGDS (FONTANILLAS CRITERIA) - ## 9.1 ## Didier's criteria 1 = SMALL / BIG - count_PAYRE = count_A+count_Y+count_P+count_R+count_E - prop_PAYRE=float(count_PAYRE)/float(ln) - count_MVGDS = count_V+count_M+count_S+count_G+count_D - prop_MVGDS=float(count_MVGDS)/float(ln) - if count_MVGDS!= 0: - ratio_PAYRE_vs_MVGDS = float(count_PAYRE)/float(count_MVGDS) - else: - ratio_PAYRE_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator) - - ## 9.2 ## Didier's criteria 2 = VERY SMALL / BIG - count_AC = count_A+count_C - prop_AC=float(count_AC)/float(ln) - - #count_VLIM = count_V+count_L+count_I+count_M - if count_MVGDS != 0: - ratio_AC_vs_MVGDS = float(count_AC)/float(count_MVGDS) - else: - ratio_AC_vs_MVGDS=-1 ## "-1" will indicate the impossibility to compute the ratio (coz the numerator) - else: - count_IVYWREL=0 - prop_IVYWREL=0 - count_ERK=0 - prop_ERK=0 - count_DNQTSH=0 - prop_DNQTSH=0 - ratio_ERK_vs_DNQTSH=0 - count_EK=0 - prop_EK=0 - count_QH=0 - prop_QH=0 - ratio_EK_vs_QH=0 - count_FYMINK=0 - prop_FYMINK=0 - count_GARP=0 - prop_GARP=0 - count_AVLIMFYW=0 - prop_AVLIMFYW=0 - count_AVLIM=0 - prop_AVLIM=0 - count_FYW=0 - prop_FYW=0 - count_STNQ=0 - prop_STNQ=0 - count_MVGDS=0 - prop_MVGDS=0 - count_PAYRE=0 - prop_PAYRE=0 - count_AC=0 - prop_AC=0 - ratio_PAYRE_vs_MVGDS=0 - ratio_AC_vs_MVGDS=0 - count_RHKDE=0 - prop_RHKDE=0 - count_RHK=0 - prop_RHK=0 - count_DE=0 - prop_DE=0 - - return(count_IVYWREL,prop_IVYWREL,count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH,count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH,count_FYMINK,prop_FYMINK,count_GARP,prop_GARP,count_AVLIMFYW, prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW,count_STNQ, prop_STNQ, count_MVGDS,prop_MVGDS, count_PAYRE,prop_PAYRE, count_AC,prop_AC, ratio_PAYRE_vs_MVGDS, ratio_AC_vs_MVGDS, count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE) -##################### - - -################## -###### DEF5 ###### -################## -def aa_properties(fileIN_aaProperties): - next = fileIN_aaProperties.readline() ## JUMP HEADERS - - bash_aa_properties={} - - while 1: - next = fileIN_aaProperties.readline() - if not next: - break - - S1 = string.split(next, ",") - - aa_name = S1[1] - S2 = string.split(aa_name, "/") - aa_code = S2[1][:-1] - - frequencies = S1[2][:-1] - Residue_Weight = S1[5] - Residue_Volume = S1[6] - Partial_specific_volume = S1[7] - Hydration = S1[8] - - bash_aa_properties[aa_code] = [frequencies,Residue_Weight,Residue_Volume,Partial_specific_volume,Hydration] - - return(bash_aa_properties) - - -################## -###### DEF6 ###### -################## -def sequence_properties_from_aa_properties(seq, bash_properties): - - ## 1 ## count occurence of AA - count_K=string.count(seq,"K") - count_R=string.count(seq,"R") - count_A=string.count(seq,"A") - count_F=string.count(seq,"F") - count_I=string.count(seq,"I") - count_L=string.count(seq,"L") - count_M=string.count(seq,"M") - count_V=string.count(seq,"V") - count_W=string.count(seq,"W") - count_N=string.count(seq,"N") - count_Q=string.count(seq,"Q") - count_S=string.count(seq,"S") - count_T=string.count(seq,"T") - count_H=string.count(seq,"H") - count_Y=string.count(seq,"Y") - count_C=string.count(seq,"C") - count_D=string.count(seq,"D") - count_E=string.count(seq,"E") - count_P=string.count(seq,"P") - count_G=string.count(seq,"G") - - TOTAL=count_K+count_R+count_A+count_F+count_I+count_L+count_M+count_V+count_W+count_N+count_Q+count_S+count_T+count_H+count_Y+count_C+count_D+count_E+count_P+count_G - - if (TOTAL!=0): - - - ## 2 ## Compute properties 1: Residue Weight (Mr) (UNIT:Daltons): - - Total_Residue_Weight = count_K*float(bash_properties["K"][1]) + count_R*float(bash_properties["R"][1]) + count_A*float(bash_properties["A"][1]) + count_F*float(bash_properties["F"][1]) + count_I*float(bash_properties["I"][1]) + count_L*float(bash_properties["L"][1]) + count_M*float(bash_properties["M"][1]) + count_V*float(bash_properties["V"][1]) + count_W*float(bash_properties["W"][1]) + count_N*float(bash_properties["N"][1]) + count_Q*float(bash_properties["Q"][1]) + count_S*float(bash_properties["S"][1]) + count_T*float(bash_properties["T"][1]) + count_H*float(bash_properties["H"][1]) + count_Y*float(bash_properties["Y"][1]) + count_C*float(bash_properties["C"][1]) + count_D*float(bash_properties["D"][1]) + count_E*float(bash_properties["E"][1]) + count_P*float(bash_properties["P"][1]) + count_G*float(bash_properties["G"][1]) - Total_Residue_Volume = count_K*float(bash_properties["K"][2]) + count_R*float(bash_properties["R"][2]) + count_A*float(bash_properties["A"][2]) + count_F*float(bash_properties["F"][2]) + count_I*float(bash_properties["I"][2]) + count_L*float(bash_properties["L"][2]) + count_M*float(bash_properties["M"][2]) + count_V*float(bash_properties["V"][2]) + count_W*float(bash_properties["W"][2]) + count_N*float(bash_properties["N"][2]) + count_Q*float(bash_properties["Q"][2]) + count_S*float(bash_properties["S"][2]) + count_T*float(bash_properties["T"][2]) + count_H*float(bash_properties["H"][2]) + count_Y*float(bash_properties["Y"][2]) + count_C*float(bash_properties["C"][2]) + count_D*float(bash_properties["D"][2]) + count_E*float(bash_properties["E"][2]) + count_P*float(bash_properties["P"][2]) + count_G*float(bash_properties["G"][2]) - Total_Partial_specific_volume = count_K*float(bash_properties["K"][3]) + count_R*float(bash_properties["R"][3]) + count_A*float(bash_properties["A"][3]) + count_F*float(bash_properties["F"][3]) + count_I*float(bash_properties["I"][3]) + count_L*float(bash_properties["L"][3]) + count_M*float(bash_properties["M"][3]) + count_V*float(bash_properties["V"][3]) + count_W*float(bash_properties["W"][3]) + count_N*float(bash_properties["N"][3]) + count_Q*float(bash_properties["Q"][3]) + count_S*float(bash_properties["S"][3]) + count_T*float(bash_properties["T"][3]) + count_H*float(bash_properties["H"][3]) + count_Y*float(bash_properties["Y"][3]) + count_C*float(bash_properties["C"][3]) + count_D*float(bash_properties["D"][3]) + count_E*float(bash_properties["E"][3]) + count_P*float(bash_properties["P"][3]) + count_G*float(bash_properties["G"][3]) - Total_Hydration = count_K*float(bash_properties["K"][4]) + count_R*float(bash_properties["R"][4]) + count_A*float(bash_properties["A"][4]) + count_F*float(bash_properties["F"][4]) + count_I*float(bash_properties["I"][4]) + count_L*float(bash_properties["L"][4]) + count_M*float(bash_properties["M"][4]) + count_V*float(bash_properties["V"][4]) + count_W*float(bash_properties["W"][4]) + count_N*float(bash_properties["N"][4]) + count_Q*float(bash_properties["Q"][4]) + count_S*float(bash_properties["S"][4]) + count_T*float(bash_properties["T"][4]) + count_H*float(bash_properties["H"][4]) + count_Y*float(bash_properties["Y"][4]) + count_C*float(bash_properties["C"][4]) + count_D*float(bash_properties["D"][4]) + count_E*float(bash_properties["E"][4]) + count_P*float(bash_properties["P"][4]) + count_G*float(bash_properties["G"][4]) - else: - Total_Residue_Weight=0 - Total_Residue_Volume=0 - Total_Partial_specific_volume=0 - Total_Hydration=0 - - return(Total_Residue_Weight,Total_Residue_Volume,Total_Partial_specific_volume,Total_Hydration) - -######################################################## - - - -################### -### RUN RUN RUN ### -################### - -##Create specific folders -Path_IN_loci_NUC = "./IN_AA" -outpath= "./OUT" -os.makedirs(Path_IN_loci_NUC) -os.makedirs(outpath) - -infiles = [] -with open(sys.argv[2], 'r') as f: - for line in f.readlines(): - infiles.append(line.strip('\n')) - -for file in infiles: - os.system("cp %s %s" %(file, Path_IN_loci_NUC)) - -## 1 ## List taxa -LT=[] -cmd="grep '>' {}".format(sys.argv[1]) -result = subprocess.check_output(cmd, shell=True) -result=result.split('\n') -for i in result: - sp=i[1:] - if sp !='': - LT.append(sp) -print LT - - -## 2 ## PathIN -fileIN_properties = open("amino_acid_properties.csv", "r") -Path_IN_loci_AA = "./IN_AA" -#Path_IN_loci_AA = "02_CDS_No_Missing_Data_aa_CDS_withM" -Lloci_AA = os.listdir(Path_IN_loci_AA) - -## 3 ## PathOUT - -## 3.1 ## PROT composition -fileOUT_PROT_ALL=open("./OUT/prot_compositions_All_AA.csv","w") -fileOUT_PROT_ALL.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_PROT_ALL.write("%s_prop_K,%s_prop_R,%s_prop_A,%s_prop_F,%s_prop_I,%s_prop_L,%s_prop_M,%s_prop_V,%s_prop_W,%s_prop_N,%s_prop_Q,%s_prop_S,%s_prop_T,%s_prop_H,%s_prop_Y,%s_prop_C,%s_prop_D,%s_prop_E,%s_prop_P,%s_prop_G," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa)) -fileOUT_PROT_ALL.write("%s_prop_K,%s_prop_R,%s_prop_A,%s_prop_F,%s_prop_I,%s_prop_L,%s_prop_M,%s_prop_V,%s_prop_W,%s_prop_N,%s_prop_Q,%s_prop_S,%s_prop_T,%s_prop_H,%s_prop_Y,%s_prop_C,%s_prop_D,%s_prop_E,%s_prop_P,%s_prop_G" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_PROT_ALL.write("\n") - -## 3.2 ## PROT IVYWREL -fileOUT_IVYWREL=open("./OUT/IVYWREL.csv","w") -fileOUT_IVYWREL.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL," %(taxa,taxa)) -fileOUT_IVYWREL.write("%s_count_IVYWREL,%s_prop_IVYWREL" %(LT[-1],LT[-1])) -fileOUT_IVYWREL.write("\n") - -## 3.3 ## PROT ERK_DNQTSHA -fileOUT_ERK_DNQTSH=open("./OUT/ERK_DNQTSH.csv","w") -fileOUT_ERK_DNQTSH.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_ERK_DNQTSH.write("%s_count_ERK,%s_prop_ERK,%s_count_DNQTSH,%s_prop_DNQTSH,%s_ratio_ERK_vs_DNQTSH," %(taxa,taxa,taxa,taxa,taxa)) -fileOUT_ERK_DNQTSH.write("%s_count_ERK,%s_prop_ERK,%s_count_DNQTSH,%s_prop_DNQTSH,%s_ratio_ERK_vs_DNQTSH" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_ERK_DNQTSH.write("\n") - -## 3.4 ## PROT EK_QH -fileOUT_EK_QH=open("./OUT/EK_QH.csv","w") -fileOUT_EK_QH.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_EK_QH.write("%s_count_EK,%s_prop_EK,%s_count_QH,%s_prop_QH,%s_ratio_EK_vs_QH," %(taxa,taxa,taxa,taxa,taxa)) -fileOUT_EK_QH.write("%s_count_EK,%s_prop_EK,%s_count_QH,%s_prop_QH,%s_ratio_EK_vs_QH" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_EK_QH.write("\n") - -## 3.5 ## PROT FYMINK_GARP -fileOUT_FYMINK_GARP=open("./OUT/FYMINK_GARP.csv","w") -fileOUT_FYMINK_GARP.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP," %(taxa,taxa,taxa,taxa)) -fileOUT_FYMINK_GARP.write("%s_count_FYMINK,%s_prop_FYMINK,%s_count_GARP,%s_prop_GARP" %(LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_FYMINK_GARP.write("\n") - -## 3.6 ## PROT AVLIMFYW -fileOUT_AVLIMFYW=open("./OUT/AVLIMFYW.csv","w") -fileOUT_AVLIMFYW.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_AVLIMFYW.write("%s_count_AVLIMFYW,%s_prop_AVLIMFYW,%s_count_AVLIM,%s_prop_AVLIM,%s_count_FYW,%s_prop_FYW," %(taxa,taxa,taxa,taxa,taxa,taxa)) -fileOUT_AVLIMFYW.write("%s_count_AVLIMFYW,%s_prop_AVLIMFYW,%s_count_AVLIM,%s_prop_AVLIM,%s_count_FYW,%s_prop_FYW" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_AVLIMFYW.write("\n") - -## 3.7 ## PROT STNQ -fileOUT_STNQ=open("./OUT/STNQ.csv","w") -fileOUT_STNQ.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ," %(taxa,taxa)) -fileOUT_STNQ.write("%s_count_STNQ,%s_prop_STNQ" %(LT[-1],LT[-1])) -fileOUT_STNQ.write("\n") - -## 3.8 ## PROT RHKDE -fileOUT_RHKDE=open("./OUT/RHKDE.csv","w") -fileOUT_RHKDE.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_RHKDE.write("%s_count_RHKDE,%s_prop_RHKDE,%s_count_RHK,%s_prop_RHK,%s_count_DE,%s_prop_DE," %(taxa,taxa,taxa,taxa,taxa,taxa)) -fileOUT_RHKDE.write("%s_count_RHKDE,%s_prop_RHKDE,%s_count_RHK,%s_prop_RHK,%s_count_DE,%s_prop_DE" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_RHKDE.write("\n") - -## 3.9 ## PROT DIDER CRITERIA -fileOUT_PAYRE=open("./OUT/PAYRE-MVGDS.csv","w") -fileOUT_PAYRE.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_PAYRE.write("%s_count_PAYRE,%s_prop_PAYRE,%s_count_AC,%s_prop_AC,%s_count_MVGDS,%s_prop_MVGDS,%s_ratio_PAYRE_vs_MVGDS,%s_ratio_AC_vs_MVGDS," %(taxa,taxa,taxa,taxa,taxa,taxa,taxa,taxa)) -fileOUT_PAYRE.write("%s_count_PAYRE,%s_prop_PAYRE,%s_count_AC,%s_prop_AC,%s_count_MVGDS,%s_prop_MVGDS,%s_ratio_PAYRE_vs_MVGDS,%s_ratio_AC_vs_MVGDS" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_PAYRE.write("\n") - -## 3.10 ## PROT Total residue weight -fileOUT_TotalResidueWeight=open("./OUT/TotalResidueWeight.csv","w") -fileOUT_TotalResidueWeight.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight," %taxa) -fileOUT_TotalResidueWeight.write("%s_Total_Residue_Weight" %LT[-1]) -fileOUT_TotalResidueWeight.write("\n") - -## 3.11 ## PROT Total residue volume -fileOUT_TotalResidueVolume=open("./OUT/TotalResidueVolume.csv","w") -fileOUT_TotalResidueVolume.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume," %taxa) -fileOUT_TotalResidueVolume.write("%s_Total_Residue_Volume" %LT[-1]) -fileOUT_TotalResidueVolume.write("\n") - -## 3.12 ## PROT Total partial specific volume -fileOUT_TotalPartialSpecificVolume=open("./OUT/TotalPartialSpecificVolume.csv","w") -fileOUT_TotalPartialSpecificVolume.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume," %taxa) -fileOUT_TotalPartialSpecificVolume.write("%s_Total_Partial_Specific_Volume" %LT[-1]) -fileOUT_TotalPartialSpecificVolume.write("\n") - -## 3.13 ## PROT Total hydratation -fileOUT_TotalHydratation=open("./OUT/TotalHydratation.csv","w") -fileOUT_TotalHydratation.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_TotalHydratation.write("%s_Total_Hydratation," %taxa) -fileOUT_TotalHydratation.write("%s_Total_Hydratation" %LT[-1]) -fileOUT_TotalHydratation.write("\n") - -##################### -## 4 ## Process Loci -##################### -bash_aa_properties = aa_properties(fileIN_properties) - -for locus in Lloci_AA: - print locus - path_locus = "%s/%s" %(Path_IN_loci_AA, locus) - bash = dico(path_locus,LT) - - #print bash - - fileOUT_PROT_ALL.write("%s," %locus) - fileOUT_IVYWREL.write("%s," %locus) - fileOUT_ERK_DNQTSH.write("%s," %locus) - fileOUT_EK_QH.write("%s," %locus) - fileOUT_FYMINK_GARP.write("%s," %locus) - fileOUT_AVLIMFYW.write("%s," %locus) - fileOUT_STNQ.write("%s," %locus) - fileOUT_RHKDE.write("%s," %locus) - fileOUT_PAYRE.write("%s," %locus) - fileOUT_TotalResidueWeight.write("%s," %locus) - fileOUT_TotalResidueVolume.write("%s," %locus) - fileOUT_TotalPartialSpecificVolume.write("%s," %locus) - fileOUT_TotalHydratation.write("%s," %locus) - - for taxa in LT[0:-1]: - if taxa in bash.keys(): - seq = bash[taxa] - prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G = aa_composition1(seq) ### DEF3 ### - count_IVYWREL,prop_IVYWREL,count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH,count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH,count_FYMINK,prop_FYMINK,count_GARP,prop_GARP,count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW,count_STNQ,prop_STNQ, count_MVGDS,prop_MVGDS, count_PAYRE,prop_PAYRE, count_AC,prop_AC, ratio_PAYRE_vs_MVGDS, ratio_AC_vs_MVGDS,count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE = aa_composition2(seq) ### DEF4 ### - Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ### - - fileOUT_PROT_ALL.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G)) - fileOUT_IVYWREL.write("%.5f,%.5f," %(count_IVYWREL, prop_IVYWREL)) - fileOUT_ERK_DNQTSH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH)) - fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f," %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH)) - fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f," %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP)) - fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW)) - fileOUT_STNQ.write("%.5f,%.5f," %(count_STNQ,prop_STNQ)) - fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE)) - fileOUT_PAYRE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f," %(count_PAYRE,prop_PAYRE,count_AC,prop_AC,count_MVGDS,prop_MVGDS,ratio_PAYRE_vs_MVGDS,ratio_AC_vs_MVGDS)) - fileOUT_TotalResidueWeight.write("%.5f," %Total_Residue_Weight) - fileOUT_TotalResidueVolume.write("%.5f," %Total_Residue_Volume) - fileOUT_TotalPartialSpecificVolume.write("%.5f," %(Total_Partial_Specific_Volume)) - fileOUT_TotalHydratation.write("%.5f," % Total_Hydration) - else: - fileOUT_PROT_ALL.write("%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA")) - fileOUT_IVYWREL.write("%s,%s," %("NA", "NA")) - fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA")) - fileOUT_EK_QH.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA")) - fileOUT_FYMINK_GARP.write("%s,%s,%s,%s," %("NA","NA","NA","NA")) - fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA")) - fileOUT_STNQ.write("%s,%s," %("NA","NA")) - fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s,"%("NA","NA","NA","NA","NA","NA")) - fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA","NA","NA","NA")) - fileOUT_TotalResidueWeight.write("%s," %"NA") - fileOUT_TotalResidueVolume.write("%s," %"NA") - fileOUT_TotalPartialSpecificVolume.write("%s," %"NA") - fileOUT_TotalHydratation.write("%s," %"NA") - - if LT[-1] in bash.keys(): - seq = bash[LT[-1]] - prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G = aa_composition1(seq) ### DEF3 ### - count_IVYWREL,prop_IVYWREL,count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH,count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH,count_FYMINK,prop_FYMINK,count_GARP,prop_GARP,count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW,count_STNQ,prop_STNQ, count_MVGDS,prop_MVGDS, count_PAYRE,prop_PAYRE, count_AC,prop_AC, ratio_PAYRE_vs_MVGDS, ratio_AC_vs_MVGDS,count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE = aa_composition2(seq) ### DEF4 ### - Total_Residue_Weight,Total_Residue_Volume,Total_Partial_Specific_Volume,Total_Hydration = sequence_properties_from_aa_properties(seq, bash_aa_properties) ### DEF6 ### - - fileOUT_PROT_ALL.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(prop_K,prop_R,prop_A,prop_F,prop_I,prop_L,prop_M,prop_V,prop_W,prop_N,prop_Q,prop_S,prop_T,prop_H,prop_Y,prop_C,prop_D,prop_E,prop_P,prop_G)) - fileOUT_IVYWREL.write("%.5f,%.5f" %(count_IVYWREL, prop_IVYWREL)) - fileOUT_ERK_DNQTSH.write("%.5f,%.5f,%.5f,%.5f,%.5f" %(count_ERK,prop_ERK,count_DNQTSH,prop_DNQTSH,ratio_ERK_vs_DNQTSH)) - fileOUT_EK_QH.write("%.5f,%.5f,%.5f,%.5f,%.5f" %(count_EK,prop_EK,count_QH,prop_QH,ratio_EK_vs_QH)) - fileOUT_FYMINK_GARP.write("%.5f,%.5f,%.5f,%.5f" %(count_FYMINK,prop_FYMINK,count_GARP,prop_GARP)) - fileOUT_AVLIMFYW.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(count_AVLIMFYW,prop_AVLIMFYW,count_AVLIM,prop_AVLIM,count_FYW,prop_FYW)) - fileOUT_STNQ.write("%.5f,%.5f" %(count_STNQ,prop_STNQ)) - fileOUT_RHKDE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f"%(count_RHKDE,prop_RHKDE,count_RHK,prop_RHK,count_DE,prop_DE)) - fileOUT_PAYRE.write("%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f,%.5f" %(count_PAYRE,prop_PAYRE,count_AC,prop_AC,count_MVGDS,prop_MVGDS,ratio_PAYRE_vs_MVGDS,ratio_AC_vs_MVGDS)) - fileOUT_TotalResidueWeight.write("%.5f" %Total_Residue_Weight) - fileOUT_TotalResidueVolume.write("%.5f" %Total_Residue_Volume) - fileOUT_TotalPartialSpecificVolume.write("%.5f" %(Total_Partial_Specific_Volume)) - fileOUT_TotalHydratation.write("%.5f" % Total_Hydration) - else: - fileOUT_PROT_ALL.write("%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA")) - fileOUT_IVYWREL.write("%s,%s" %("NA", "NA")) - fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA")) - fileOUT_EK_QH.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA")) - fileOUT_FYMINK_GARP.write("%s,%s,%s,%s" %("NA","NA","NA","NA")) - fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA")) - fileOUT_STNQ.write("%s,%s" %("NA","NA")) - fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s"%("NA","NA","NA","NA","NA","NA")) - fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA","NA","NA","NA")) - fileOUT_TotalResidueWeight.write("%s" %"NA") - fileOUT_TotalResidueVolume.write("%s" %"NA") - fileOUT_TotalPartialSpecificVolume.write("%s" %"NA") - fileOUT_TotalHydratation.write("%s" %"NA") - - ## END LINE - fileOUT_PROT_ALL.write("\n") - fileOUT_IVYWREL.write("\n") - fileOUT_ERK_DNQTSH.write("\n") - fileOUT_EK_QH.write("\n") - fileOUT_FYMINK_GARP.write("\n") - fileOUT_AVLIMFYW.write("\n") - fileOUT_STNQ.write("\n") - fileOUT_RHKDE.write("\n") - fileOUT_PAYRE.write("\n") - fileOUT_TotalResidueWeight.write("\n") - fileOUT_TotalResidueVolume.write("\n") - fileOUT_TotalPartialSpecificVolume.write("\n") - fileOUT_TotalHydratation.write("\n") -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S02b_extreme_2states.py Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,159 @@ +#!/usr/bin/env python +#coding: utf-8 +#Author : Eric Fontanillas (2010) - Victor Mataigne (2018) + +import pandas as pd +import argparse, os + +def loop_on_elems(list_of_elems, path_in, path_out, sps_group_1, sps_group_2, colnames): + + # sub-routine + + def tableu(fileu, sps_group_1, sps_group_2): + """ a + + Args : + fileu : input file with counts of AAs / AAs types per orthogorup + sps_group_1 : species for condition 1 (ex : hot water species) + sps_group_2 : species for condition 2 (ex : cold water species) + + Returns : + greater_dict : + lower_dict : + + """ + df = pd.read_csv(fileu, sep=',', index_col=0, header=0) + # species = list(df) #columns names = species names + + # initialize counts + greater_dict = {} + lower_dict = {} + + for specie in sps_group_1+sps_group_2: + greater_dict[specie] = 0 + lower_dict[specie] = 0 + + #nb_trials = 0 + for (index, row) in df.iterrows(): + # min and max counts for each condition + if not df.loc[index, sps_group_1+sps_group_2].isnull().values.any() : + #nb_trials += 1 + + max_cat1 = max(df.loc[index, sps_group_1]) # species in category 1 (ex : hots) + min_cat1 = min(df.loc[index, sps_group_1]) + max_cat2 = max(df.loc[index, sps_group_2]) # species in category 2 (ex : colds) + min_cat2 = min(df.loc[index, sps_group_2]) + + for specie in sps_group_1: + if df.loc[index, specie] > max_cat2 : + greater_dict[specie] += 1 + elif df.loc[index, specie] < min_cat2 : + lower_dict[specie] += 1 + + for specie in sps_group_2: + if df.loc[index, specie] > max_cat1 : + greater_dict[specie] += 1 + elif df.loc[index, specie] < min_cat1 : + lower_dict[specie] += 1 + + return greater_dict, lower_dict#, nb_trials + + # Function ------------------------------------------------------ + + for variable in list_of_elems: + print 'Processing : {} ...'.format(variable) + file_in = "{}/{}.csv".format(path_in, variable) + file_out = open('{}/{}.csv'.format(path_out,variable), 'w') + + # Compute succeses and fails on each variable + greater_dict, lower_dict = tableu(file_in, sps_group_1, sps_group_2) + + # totals and diffs + diff_dict = {} + total_dict = {} + for key in greater_dict.keys(): + diff_dict[key] = greater_dict[key] - lower_dict[key] + total_dict[key] = greater_dict[key] + lower_dict[key] + #total_dict[key] = number_trials + + # results frame + df = pd.DataFrame([greater_dict, lower_dict, diff_dict, total_dict]) + df = df.rename({0:'Greater',1:'Lower',2:'Difference',3:'Trial_Number'}) #, axis='index' if pandas 0.15 + df = df.rename(index=str, columns=colnames) + + df.to_csv("{}/{}.csv".format(path_out, variable), sep=",", encoding="utf-8") + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("sps_group_1", help="List of species separated by commas") + parser.add_argument("sps_group_2", help="List of species separated by commas") + parser.add_argument("format", choices=['nucleic', 'proteic'], help="input files format") + args = parser.parse_args() + + # used only if format = nucleic + LN =['A','C','T','G'] + Lratios = ['GC_percent', 'purine_percent', 'DIFF_GC', 'DIFF_AT', 'PLI_GC', 'PLI_AT', 'PLI_GC_1000', 'PLI_AT_1000'] + + # used only if format = proteic + LAA =['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G'] + LV = ['IVYWREL','EK','ERK','DNQTSHA','QH','ratio_ERK_DNQTSHA','ratio_EK_QH','FYMINK','GARP', + 'ratio_GARP_FYMINK','AVLIM','FYW','AVLIMFYW','STNQ','RHK','DE','RHKDE','APGC','AC', + 'VLIM','ratio_AC_VLIM','ratio_APGC_VLIM'] + LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation'] + + # inputs and outputs paths + if args.format == 'nucleic': + input_path_elem = '02_tables_per_nucleotide' + input_path_var = '02_tables_per_nuc_variable' + out_path_elem = '03_tables_counts_signTest_nucleotides' + out_path_var = '03_tables_counts_signTest_nuc_variables' + elif args.format == 'proteic': + input_path_elem = '02_tables_per_aa' + input_path_var = '02_tables_per_aa_variable' + out_path_elem = '03_tables_counts_signTest_aa' + out_path_var = '03_tables_counts_signTest_aa_variables' + + os.mkdir(out_path_elem) + os.mkdir(out_path_var) + + sps_group_1 = args.sps_group_1.split(',') + sps_group_2 = args.sps_group_2.split(',') + + # Prepare colnames for final frames + colnames = {} + # for specie in sps_group_1: + # colnames[specie] = '{}_vs_condition_1'.format(specie) + # for specie in sps_group_2: + # colnames[specie] = '{}_vs_condition_2'.format(specie) + + for specie in sps_group_1: + colnames[specie] = '{}_vs_{}'.format(specie, args.sps_group_2.replace(',','')) + for specie in sps_group_2: + colnames[specie] = '{}_vs_{}'.format(specie, args.sps_group_1.replace(',','')) + + # Building tables + if args.format == 'nucleic': + loop_on_elems(LN, input_path_elem, out_path_elem, sps_group_1, sps_group_2, colnames) + loop_on_elems(Lratios, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames) + elif args.format == 'proteic': + loop_on_elems(LAA, input_path_elem, out_path_elem, sps_group_1, sps_group_2, colnames) + loop_on_elems(LV, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames) + loop_on_elems(LS, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames) + + # Final R script launching sign test + print 'Processing : binomial sign tests ...' + + if args.format == 'nucleic': + final_output_elem = '04_outputs_nucleotides' + final_output_var = '04_outputs_nuc_variables' + elif args.format == 'proteic': + final_output_elem = '04_outputs_aa' + final_output_var = '04_outputs_aa_variables' + + os.mkdir(final_output_elem) + os.mkdir(final_output_var) + os.system('Rscript S03b_sign_test_binomial.R --indir %s --outdir %s' %(out_path_elem, final_output_elem)) + os.system('Rscript S03b_sign_test_binomial.R --indir %s --outdir %s' %(out_path_var, final_output_var)) + +if __name__ == '__main__': + main()
--- a/scripts/S02b_study_seq_composition_nuc.py Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,205 +0,0 @@ -#!/usr/bin/env python -## Author: Eric FONTANILLAS -## Date: 21.12.10 -## Last Version : 12/2017 by Victor Mataigne -## Object: Test for compositional bias in genome and proteome as marker of thermal adaptation (comparison between 2 "hot" species: Ap and Ps and one "cold" species: Pg) - -import sys,os,shutil,subprocess, string, itertools -from functions import simplify_fasta_name, dico - -################## -###### DEF2 ###### -################## -def base_composition(seq): - count_A=string.count(seq, "A") + string.count(seq, "a") - count_T=string.count(seq, "T") + string.count(seq, "t") - count_C=string.count(seq, "C") + string.count(seq, "c") - count_G=string.count(seq, "G") + string.count(seq, "g") - ## 3 ## Nucleotide proportions - ln = count_C+count_G+count_T+count_A - if (ln!=0): - - CG = count_C+count_G - AT = count_T+count_A - - AG = count_A+count_G - TC = count_T+count_C - - ## 1 ## Search for compositional bias in genome as marker of thermal adaptation: CG vs AT - ratio_CG_AT = float(CG)/float(AT) - percent_CG = float(CG)/(float(AT) + float(CG))*100 - - ## 2 ## Search for compositional bias in genome as marker of thermal adaptation: AG vs TC - ratio_purine_pyrimidine=float(AG)/float(TC) - percent_purine=float(AG)/(float(AG)+float(TC))*100 - - - prop_A = float(count_A)/float(ln) - prop_T = float(count_T)/float(ln) - prop_C = float(count_C)/float(ln) - prop_G = float(count_G)/float(ln) - else: - percent_CG=0 - percent_purine=0 - prop_A=0 - prop_T=0 - prop_C=0 - prop_G=0 - - return(percent_CG, percent_purine, prop_A, prop_T, prop_C, prop_G) -############################################## - -################## -###### DEF3 ###### -################## -def purine_loading(seq): - count_A=string.count(seq, "A") + string.count(seq, "a") - count_T=string.count(seq, "T") + string.count(seq, "t") - count_C=string.count(seq, "C") + string.count(seq, "c") - count_G=string.count(seq, "G") + string.count(seq, "g") - ## 3 ## Nucleotide proportions - TOTAL = count_C+count_G+count_T+count_A - if (TOTAL!=0): - - ## PLI : Purine loading indice (Forsdyke et al.) - # (G-C)/N * 1000 et (A-T)/N * 1000 - - DIFF_GC = count_G - count_C - DIFF_AT = count_A - count_T - - # Per bp - PLI_GC = float(DIFF_GC)/float(TOTAL) - PLI_AT = float(DIFF_AT)/float(TOTAL) - - # Per 1000 bp - PLI_GC_1000 = PLI_GC*1000 - PLI_AT_1000 = PLI_AT*1000 - else: - DIFF_GC=0 - DIFF_AT=0 - PLI_GC=0 - PLI_AT=0 - PLI_GC_1000=0 - PLI_AT_1000=0 - - return(TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000) -############################################## - -################### -### RUN RUN RUN ### -################### - -##Create specific folders -Path_IN_loci_NUC = "./IN_NUC" -outpath= "./OUT" -os.makedirs(Path_IN_loci_NUC) -os.makedirs(outpath) - -infiles = [] -with open(sys.argv[2], 'r') as f: - for line in f.readlines(): - infiles.append(line.strip('\n')) - -#infiles = str.split(sys.argv[1], ",") -for file in infiles: - os.system("cp %s %s" %(file, Path_IN_loci_NUC)) - -## 1 ## List taxa -LT=[] -cmd="grep '>' {}".format(sys.argv[1]) -result = subprocess.check_output(cmd, shell=True) -result=result.split('\n') -for i in result: - sp=i[1:] - if sp !='': - LT.append(sp) -print LT - -## 2 ## PathIN -Lloci_NUC = os.listdir(Path_IN_loci_NUC) - - -## 3 ## PathOUT -## 3.1 ## NUC composition -fileOUT_NUC=open("./OUT/nuc_compositions.csv","w") -fileOUT_NUC.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G," %(taxa,taxa,taxa,taxa)) -fileOUT_NUC.write("%s_prop_A,%s_prop_T,%s_prop_C,%s_prop_G" %(LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_NUC.write("\n") - -## 3.2 ## NUC percent_GC -fileOUT_percent_GC=open("./OUT/percent_GC.csv","w") -fileOUT_percent_GC.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_percent_GC.write("%s_percent_GC," %(taxa)) -fileOUT_percent_GC.write("%s_percentGC" %(LT[-1])) -fileOUT_percent_GC.write("\n") - -## 3.3 ## NUC percent_purine -fileOUT_percent_purine=open("./OUT/percent_purine.csv","w") -fileOUT_percent_purine.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_percent_purine.write("%s_percent_purine," %(taxa)) -fileOUT_percent_purine.write("%s_percent_purine" %(LT[-1])) -fileOUT_percent_purine.write("\n") - -## 3.4 ## Purine Load -fileOUT_Purine_Load=open("./OUT/Purine_Load_Indice.csv", "w") -fileOUT_Purine_Load.write("LOCUS,") -for taxa in LT[0:-1]: - fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000," %(taxa,taxa,taxa,taxa,taxa)) -fileOUT_Purine_Load.write("%s_TOTAL,%s_DIFF_GC,%s_DIFF_AT,%s_PLI_GC1000,%s_PLI_AT1000" %(LT[-1],LT[-1],LT[-1],LT[-1],LT[-1])) -fileOUT_Purine_Load.write("\n") - -##################### -## 4 ## Process Loci -##################### -for locus in Lloci_NUC: - print locus - path_locus = "%s/%s" %(Path_IN_loci_NUC, locus) - bash = dico(path_locus,LT) - - fileOUT_NUC.write("%s," %locus) - fileOUT_percent_GC.write("%s," %locus) - fileOUT_percent_purine.write("%s," %locus) - fileOUT_Purine_Load.write("%s," %locus) - - for taxa in LT[0:-1]: - if taxa in bash.keys(): - seq = bash[taxa] - percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ### - TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ### - fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f," %(prop_A,prop_T,prop_C,prop_G)) - fileOUT_percent_GC.write("%.5f," %percent_GC) - fileOUT_percent_purine.write("%.5f," %percent_purine) - fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f," %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000)) - else: - fileOUT_NUC.write("%s,%s,%s,%s," %("NA","NA","NA","NA")) - fileOUT_percent_GC.write("%s," %"NA") - fileOUT_percent_purine.write("%s," %"NA") - fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("NA","NA","NA","NA","NA")) - - if LT[-1] in bash.keys(): - seq = bash[LT[-1]] - percent_GC, percent_purine,prop_A, prop_T, prop_C, prop_G = base_composition(seq) ### DEF2 ### - TOTAL, DIFF_GC, DIFF_AT,PLI_GC,PLI_AT,PLI_GC_1000,PLI_AT_1000 = purine_loading(seq) ### DEF3 ### - fileOUT_NUC.write("%.5f,%.5f,%.5f,%.5f" %(prop_A,prop_T,prop_C,prop_G)) - fileOUT_percent_GC.write("%.5f" %percent_GC) - fileOUT_percent_purine.write("%.5f" %percent_purine) - fileOUT_Purine_Load.write("%d,%d,%d,%.5f,%.5f" %(TOTAL, DIFF_GC, DIFF_AT,PLI_GC_1000, PLI_AT_1000)) - else: - fileOUT_NUC.write("%s,%s,%s,%s" %("NA","NA","NA","NA")) - fileOUT_percent_GC.write("%s" %"NA") - fileOUT_percent_purine.write("%s" %"NA") - fileOUT_Purine_Load.write("%s,%s,%s,%s,%s" %("NA","NA","NA","NA","NA")) - - - fileOUT_NUC.write("\n") - fileOUT_percent_GC.write("\n") - fileOUT_percent_purine.write("\n") - fileOUT_Purine_Load.write("\n") -fileOUT_NUC.close() -fileOUT_percent_GC.close() -fileOUT_percent_purine.close() -fileOUT_Purine_Load.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S03b_sign_test_binomial.R Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,56 @@ +#!/usr/bin/env Rscript +#coding: utf-8 +#Author : Eric Fontanillas (2010) - Victor Mataigne (2018) + +# binom test - null hypothesis : +# The test computes the number of times where the value of the variable A is higher to the value of the variable B. +# Under the null hypothesis, there is no difference between variables : A > B in 50% of the trials + +options(warn = -1) + +library(optparse) + +option_list = list( + make_option(c('-i', '--indir'), type='character', default=NULL, help='input directory name', metavar='character'), + make_option(c('-o', '--outdir'), type='character', default=NULL, help='output directory name', metavar='character') +); + +opt_parser = OptionParser(option_list=option_list); +opt = parse_args(opt_parser); +path_IN <- opt$indir +path_OUT <- opt$outdir +files_OUT <- paste(path_OUT,"/*",sep='') +unlink(files_OUT) ### clean the path_OUT folder from previous files +list_files <- list.files(path_IN) + +# iterate over file +for(file in list_files){ + name_OUT = paste(path_OUT,"/", file, sep='') + name_IN = paste(path_IN,"/", file, sep='') + + b <- read.table(name_IN, sep=",", header=T, row.names=1) + + supplemental_cells <- matrix(0, nrow=4, ncol=ncol(b)) + colnames(supplemental_cells) <- colnames(b) + row.names(supplemental_cells) <- c('p-value', 'probability_of_success', 'confidence_interval_low', 'confidence_interval_high') + + # iterate over species groups + for (i in 1:ncol(b)) { + if (b[4,i] != 0) { + binom_test <- binom.test(b[1,i], b[4,i]) + supplemental_cells[1,i] <- binom_test$p.value + supplemental_cells[2,i] <- binom_test$estimate + supplemental_cells[3,i] <- binom_test$conf.int[1] + supplemental_cells[4,i] <- binom_test$conf.int[2] + } else { + supplemental_cells[1,i] <- NA + supplemental_cells[2,i] <- NA + supplemental_cells[3,i] <- NA + supplemental_cells[4,i] <- NA + } + } + + final <- rbind(b, supplemental_cells) + write.csv(final, file=name_OUT) +} +
--- a/scripts/functions.py Tue Jul 03 10:55:46 2018 -0400 +++ b/scripts/functions.py Mon Sep 24 04:34:39 2018 -0400 @@ -1,33 +1,65 @@ -import itertools +#!/usr/bin/env python +#coding: utf-8 + +import itertools, os + +def dico(fasta_file, path_in): + """ + Stores a fasta file in a dictionary : key/value -> header/sequence + + Args: + - fasta_file (String) : the name of fasta file + - path_in (String) : path to the fasta file -def simplify_fasta_name(fasta_name,LT): - for abbreviation in LT: - if abbreviation in fasta_name: - new_fasta_name = abbreviation + Return: + - bash1 (dict) : the dictionary header/sequence + """ + bash1 = {} - return(new_fasta_name) + with open(path_in+'/'+fasta_file, 'r') as F1: + for h,s in itertools.izip_longest(*[F1]*2): + fasta_name = h[1:3] + sequence = s[:-1] + if fasta_name not in bash1.keys(): + bash1[fasta_name] = sequence + else: + print fasta_name + + return bash1 # same length for all (alignment) + +def write_output(names, sps_list, out_dir, results_dict): + """ Write results in csv files. There is one file per counted element (one file per amino-acid, one file per indice ...) -## Generates bash, with key = fasta name; value = sequence (WITH GAP, IF ANY, REMOVED IN THIS FUNCTION) -def dico(fasta_file,LT): - #count_fastaName = 0 - bash1 = {} - with open(fasta_file, "r") as file: - for name, query in itertools.izip_longest(*[file]*2): - if not name: - break - if name[0] == ">": - #count_fastaName += 1 - fasta_name = name[1:-1] - sequence = query[:-1] - if fasta_name not in bash1.keys(): - fasta_name = simplify_fasta_name(fasta_name, LT) - bash1[fasta_name] = sequence - else : - print fasta_name + Args: + - names (list) : list with the names of elems + - sps_list (list) : species names, sorted alphabetically + - out_dir (String) : output directory + - results_dict (dict) : vcounts values of each element for each input file (keys names : elems from 'names argument') - kk = bash1.keys() - key0 = kk[0] - seq0 = bash1[key0] - ln_seq = len(seq0) - - return(bash1) \ No newline at end of file + """ + for name in names: + out = open(name+".csv", 'w') + out.write('Group,' + sps_list[0:-1]+'\n') + for group in results_dict.keys(): + count_of_elems = '' + for specs in sorted(results_dict[group].keys()): + count_of_elems += str(results_dict[group][specs][name]) + ',' + out.write(group + ',' + count_of_elems[0:-1] + '\n') + out.close() + os.system('mv %s.csv %s/' %(name, out_dir)) + +def fill_with_NaN(what): + """ Used to create a dict only with NaN values ; used when a species is not present in an orthogroup + + Args: + - what (list of Strings) : the names of the elements studied (nucleotide, amino-acids, indices of thermostability ...) + + Return: + - NaN_values (dict) : dictionary with keys=elems of what, values=NaN + """ + + NaN_values = {} + for elem in what: + NaN_values[elem] = 'NaN' + + return NaN_values
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/A.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,2,2,2,2,2 +locus_6sp_60.fasta,2,2,2,2,2,2 +locus_6sp_40.fasta,8,7,7,6,8,7 +locus_6sp_58.fasta,1,1,0,0,1,0 +locus_6sp_38.fasta,4,4,5,4,2,3 +locus_4sp_4.fasta,3,NaN,2,2,2,NaN +locus_4sp_6.fasta,0,1,0,0,NaN,NaN +locus_6sp_27.fasta,1,1,1,0,1,0 +locus_6sp_41.fasta,5,5,5,5,6,5 +locus_6sp_39.fasta,3,3,4,3,3,4 +locus_6sp_10.fasta,5,5,5,5,4,5 +locus_6sp_25.fasta,19,18,20,17,19,18 +locus_6sp_32.fasta,8,8,10,8,8,10 +locus_6sp_53.fasta,7,6,6,6,6,7 +locus_3sp_2.fasta,NaN,3,NaN,3,4,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,4,3,3,3,4,3 +locus_6sp_11.fasta,14,14,12,13,13,13 +locus_6sp_35.fasta,3,3,4,3,3,3 +locus_6sp_46.fasta,7,7,7,6,5,8 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,9,9,8,7,8,9 +locus_6sp_50.fasta,35,34,35,37,36,36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/C.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,1,1,1,1,1,1 +locus_6sp_40.fasta,0,0,1,0,0,1 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,0,0 +locus_4sp_4.fasta,3,NaN,5,4,5,NaN +locus_4sp_6.fasta,13,13,13,13,NaN,NaN +locus_6sp_27.fasta,1,2,2,2,1,2 +locus_6sp_41.fasta,2,2,2,2,2,2 +locus_6sp_39.fasta,0,0,0,0,0,0 +locus_6sp_10.fasta,3,3,3,3,3,3 +locus_6sp_25.fasta,1,1,1,1,1,1 +locus_6sp_32.fasta,1,1,1,1,1,1 +locus_6sp_53.fasta,0,0,0,0,0,1 +locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN +locus_6sp_47.fasta,0,0,0,0,0,0 +locus_6sp_16.fasta,1,1,1,1,1,1 +locus_6sp_11.fasta,2,2,2,2,2,2 +locus_6sp_35.fasta,5,5,2,4,3,4 +locus_6sp_46.fasta,0,0,0,0,0,0 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,1,1,1,1,1,1 +locus_6sp_50.fasta,3,3,3,3,3,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/D.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,2,2,2,3,2,2 +locus_6sp_40.fasta,6,5,4,4,6,3 +locus_6sp_58.fasta,3,3,3,3,3,3 +locus_6sp_38.fasta,5,5,4,6,6,5 +locus_4sp_4.fasta,1,NaN,2,1,2,NaN +locus_4sp_6.fasta,7,7,6,7,NaN,NaN +locus_6sp_27.fasta,1,1,1,1,0,1 +locus_6sp_41.fasta,2,2,2,2,2,2 +locus_6sp_39.fasta,2,2,2,2,2,2 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,23,23,23,23,22,24 +locus_6sp_32.fasta,7,7,6,6,7,5 +locus_6sp_53.fasta,4,4,4,3,3,5 +locus_3sp_2.fasta,NaN,4,NaN,3,3,NaN +locus_6sp_47.fasta,4,4,4,4,4,4 +locus_6sp_16.fasta,3,3,3,2,5,3 +locus_6sp_11.fasta,9,9,9,8,8,8 +locus_6sp_35.fasta,1,1,1,1,1,1 +locus_6sp_46.fasta,4,4,3,4,4,3 +locus_3sp_7.fasta,4,5,4,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,4,4,5,4,5,4 +locus_6sp_50.fasta,7,8,7,7,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/E.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,2,2,2,1,2,2 +locus_6sp_40.fasta,7,8,9,8,7,9 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,7,7,8,6,6,7 +locus_4sp_4.fasta,1,NaN,1,1,1,NaN +locus_4sp_6.fasta,7,7,8,7,NaN,NaN +locus_6sp_27.fasta,0,0,2,0,1,0 +locus_6sp_41.fasta,1,1,1,1,1,1 +locus_6sp_39.fasta,5,4,5,4,4,5 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,18,18,19,17,17,18 +locus_6sp_32.fasta,12,12,13,15,12,14 +locus_6sp_53.fasta,13,13,13,13,12,12 +locus_3sp_2.fasta,NaN,1,NaN,2,1,NaN +locus_6sp_47.fasta,2,2,2,2,2,2 +locus_6sp_16.fasta,6,6,5,6,6,5 +locus_6sp_11.fasta,13,13,13,14,13,13 +locus_6sp_35.fasta,1,1,1,1,1,1 +locus_6sp_46.fasta,22,22,24,22,22,23 +locus_3sp_7.fasta,3,2,3,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,3,2 +locus_6sp_57.fasta,8,8,7,8,7,8 +locus_6sp_50.fasta,4,3,3,4,3,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/F.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,3,3,3,3,3,3 +locus_6sp_40.fasta,2,2,2,2,2,2 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,1,1,1,1,2,1 +locus_4sp_4.fasta,5,NaN,6,7,7,NaN +locus_4sp_6.fasta,2,2,2,1,NaN,NaN +locus_6sp_27.fasta,3,3,1,1,2,2 +locus_6sp_41.fasta,4,4,4,5,5,5 +locus_6sp_39.fasta,5,6,6,6,4,6 +locus_6sp_10.fasta,6,6,6,6,7,6 +locus_6sp_25.fasta,15,15,15,16,15,16 +locus_6sp_32.fasta,8,8,9,9,9,9 +locus_6sp_53.fasta,11,11,11,10,11,9 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,0,0,0,0,0,0 +locus_6sp_16.fasta,2,2,1,2,2,1 +locus_6sp_11.fasta,6,6,6,5,7,6 +locus_6sp_35.fasta,8,8,9,7,8,11 +locus_6sp_46.fasta,7,6,6,6,6,6 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,1,1,2,2,1,2 +locus_6sp_50.fasta,9,9,10,9,9,9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/G.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,3,3,3,3 +locus_6sp_60.fasta,3,3,3,4,3,3 +locus_6sp_40.fasta,9,9,10,10,9,10 +locus_6sp_58.fasta,4,4,4,4,4,4 +locus_6sp_38.fasta,3,3,3,3,3,3 +locus_4sp_4.fasta,1,NaN,1,1,1,NaN +locus_4sp_6.fasta,6,6,6,6,NaN,NaN +locus_6sp_27.fasta,1,1,0,0,1,1 +locus_6sp_41.fasta,3,3,3,3,3,3 +locus_6sp_39.fasta,2,2,2,2,3,2 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,24,24,25,25,23,25 +locus_6sp_32.fasta,6,6,6,6,7,6 +locus_6sp_53.fasta,9,9,9,9,10,9 +locus_3sp_2.fasta,NaN,4,NaN,4,4,NaN +locus_6sp_47.fasta,7,7,7,7,8,7 +locus_6sp_16.fasta,5,5,5,5,5,5 +locus_6sp_11.fasta,15,15,15,14,15,15 +locus_6sp_35.fasta,5,5,5,6,5,6 +locus_6sp_46.fasta,4,4,4,3,3,3 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,8,8,8,8,8,8 +locus_6sp_50.fasta,39,39,39,39,40,39
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/H.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,2,2,2,3,2,3 +locus_6sp_58.fasta,1,1,1,2,1,1 +locus_6sp_38.fasta,11,11,10,10,8,10 +locus_4sp_4.fasta,6,NaN,4,4,5,NaN +locus_4sp_6.fasta,2,3,2,3,NaN,NaN +locus_6sp_27.fasta,3,3,3,3,2,3 +locus_6sp_41.fasta,1,1,1,1,0,1 +locus_6sp_39.fasta,4,4,4,4,3,4 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,10,10,11,10,10,11 +locus_6sp_32.fasta,1,1,2,2,1,1 +locus_6sp_53.fasta,3,3,5,3,3,1 +locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,1,1,1,1,1,1 +locus_6sp_11.fasta,0,1,1,1,1,0 +locus_6sp_35.fasta,2,2,2,2,2,3 +locus_6sp_46.fasta,0,0,0,0,0,0 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,2,2,2,2,2,2 +locus_6sp_50.fasta,2,2,2,3,3,2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/I.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,1,1,1,1,1,1 +locus_6sp_40.fasta,5,4,5,3,5,4 +locus_6sp_58.fasta,1,1,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,1,0 +locus_4sp_4.fasta,7,NaN,9,9,9,NaN +locus_4sp_6.fasta,6,7,6,6,NaN,NaN +locus_6sp_27.fasta,0,0,1,1,3,2 +locus_6sp_41.fasta,5,5,5,6,5,6 +locus_6sp_39.fasta,4,3,4,3,4,4 +locus_6sp_10.fasta,5,5,5,5,5,5 +locus_6sp_25.fasta,17,16,15,15,15,15 +locus_6sp_32.fasta,5,4,2,3,1,2 +locus_6sp_53.fasta,8,8,6,8,6,8 +locus_3sp_2.fasta,NaN,0,NaN,1,0,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,3,3,3,4,4,3 +locus_6sp_11.fasta,10,11,12,10,10,11 +locus_6sp_35.fasta,4,5,4,7,7,4 +locus_6sp_46.fasta,10,10,11,9,10,10 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,3,3,3,3,4,3 +locus_6sp_50.fasta,23,22,24,20,20,24
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/K.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,1,1,0,1,1,0 +locus_6sp_40.fasta,9,8,10,10,9,10 +locus_6sp_58.fasta,1,1,1,1,1,1 +locus_6sp_38.fasta,15,15,15,15,15,15 +locus_4sp_4.fasta,1,NaN,1,1,0,NaN +locus_4sp_6.fasta,5,5,8,6,NaN,NaN +locus_6sp_27.fasta,1,1,0,1,0,1 +locus_6sp_41.fasta,1,2,1,1,1,1 +locus_6sp_39.fasta,4,3,3,3,4,3 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,18,17,20,20,21,19 +locus_6sp_32.fasta,19,20,19,19,19,19 +locus_6sp_53.fasta,11,11,10,10,11,10 +locus_3sp_2.fasta,NaN,4,NaN,4,4,NaN +locus_6sp_47.fasta,10,10,10,10,10,10 +locus_6sp_16.fasta,2,2,2,2,2,2 +locus_6sp_11.fasta,16,16,15,15,15,15 +locus_6sp_35.fasta,2,2,2,2,2,2 +locus_6sp_46.fasta,23,24,25,22,26,24 +locus_3sp_7.fasta,4,4,4,NaN,NaN,NaN +locus_6sp_30.fasta,4,4,4,4,3,3 +locus_6sp_57.fasta,5,5,5,5,5,5 +locus_6sp_50.fasta,7,5,6,6,6,6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/L.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,4,3,2,3 +locus_6sp_60.fasta,2,2,1,1,2,1 +locus_6sp_40.fasta,8,7,9,10,9,9 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,1,1,0,0,0,0 +locus_4sp_4.fasta,11,NaN,10,8,10,NaN +locus_4sp_6.fasta,4,4,5,4,NaN,NaN +locus_6sp_27.fasta,9,9,8,9,10,8 +locus_6sp_41.fasta,7,7,7,6,8,8 +locus_6sp_39.fasta,3,3,3,3,5,3 +locus_6sp_10.fasta,2,2,3,2,3,3 +locus_6sp_25.fasta,25,24,24,25,24,26 +locus_6sp_32.fasta,13,14,14,13,14,14 +locus_6sp_53.fasta,6,6,7,7,7,9 +locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN +locus_6sp_47.fasta,6,6,6,6,6,6 +locus_6sp_16.fasta,3,3,3,3,3,3 +locus_6sp_11.fasta,11,11,11,11,11,11 +locus_6sp_35.fasta,8,8,8,6,6,7 +locus_6sp_46.fasta,14,13,13,14,14,13 +locus_3sp_7.fasta,8,8,8,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,8,8,8,8,8,8 +locus_6sp_50.fasta,27,27,26,27,26,26
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/M.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,2,3,3,3 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,9,9,9,9,9,9 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,0,0 +locus_4sp_4.fasta,2,NaN,2,2,5,NaN +locus_4sp_6.fasta,2,2,2,2,NaN,NaN +locus_6sp_27.fasta,0,0,0,1,0,0 +locus_6sp_41.fasta,2,2,2,1,2,1 +locus_6sp_39.fasta,0,0,0,1,0,0 +locus_6sp_10.fasta,5,5,4,5,4,4 +locus_6sp_25.fasta,3,3,3,4,6,4 +locus_6sp_32.fasta,7,7,7,7,9,7 +locus_6sp_53.fasta,1,1,1,1,1,2 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,0,1,0,0,0,0 +locus_6sp_16.fasta,0,0,0,0,0,0 +locus_6sp_11.fasta,6,5,6,6,4,6 +locus_6sp_35.fasta,1,1,2,1,1,2 +locus_6sp_46.fasta,4,4,2,4,3,3 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,4,4,4,4,4,4 +locus_6sp_50.fasta,18,18,19,20,20,20
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/N.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,1,1,2,2,1,2 +locus_6sp_40.fasta,1,1,0,1,0,1 +locus_6sp_58.fasta,1,1,1,1,2,1 +locus_6sp_38.fasta,5,5,5,5,5,5 +locus_4sp_4.fasta,1,NaN,1,3,1,NaN +locus_4sp_6.fasta,6,5,4,4,NaN,NaN +locus_6sp_27.fasta,0,0,0,0,0,0 +locus_6sp_41.fasta,3,2,2,2,2,3 +locus_6sp_39.fasta,2,2,2,2,2,2 +locus_6sp_10.fasta,1,1,1,1,1,1 +locus_6sp_25.fasta,17,19,14,13,17,13 +locus_6sp_32.fasta,3,3,3,3,3,3 +locus_6sp_53.fasta,4,4,4,4,3,5 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,0,0,1,1,0,0 +locus_6sp_11.fasta,6,6,7,7,8,7 +locus_6sp_35.fasta,3,3,1,2,3,2 +locus_6sp_46.fasta,3,3,3,3,4,3 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,2,2,3,3,2,3 +locus_6sp_50.fasta,6,6,7,7,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/P.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,4,4,3,4,4,4 +locus_6sp_58.fasta,0,0,0,1,0,0 +locus_6sp_38.fasta,8,7,7,7,7,7 +locus_4sp_4.fasta,3,NaN,3,3,4,NaN +locus_4sp_6.fasta,4,4,4,4,NaN,NaN +locus_6sp_27.fasta,1,1,2,0,0,2 +locus_6sp_41.fasta,1,1,1,1,1,1 +locus_6sp_39.fasta,2,2,2,2,2,2 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,16,15,14,15,14,14 +locus_6sp_32.fasta,4,4,4,4,5,4 +locus_6sp_53.fasta,6,6,6,6,6,5 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,0,0,0,0,0,0 +locus_6sp_16.fasta,1,1,1,1,1,1 +locus_6sp_11.fasta,6,6,6,5,6,6 +locus_6sp_35.fasta,4,4,3,4,3,3 +locus_6sp_46.fasta,2,2,2,2,2,2 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,2,2,2,2,2,2 +locus_6sp_50.fasta,13,13,13,13,13,13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/Q.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,2,2,2,1,2,1 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,2,2,2,2,2,1 +locus_4sp_4.fasta,0,NaN,0,0,0,NaN +locus_4sp_6.fasta,4,4,4,4,NaN,NaN +locus_6sp_27.fasta,2,2,1,2,3,2 +locus_6sp_41.fasta,2,2,2,2,3,2 +locus_6sp_39.fasta,3,4,2,3,4,2 +locus_6sp_10.fasta,1,1,1,1,1,1 +locus_6sp_25.fasta,11,11,10,10,11,8 +locus_6sp_32.fasta,4,3,4,2,3,4 +locus_6sp_53.fasta,4,4,3,5,4,5 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,1,1,2,1,1,2 +locus_6sp_11.fasta,9,8,8,7,7,9 +locus_6sp_35.fasta,0,0,0,0,0,0 +locus_6sp_46.fasta,6,5,6,8,8,7 +locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,3,3,3,3,3,3 +locus_6sp_50.fasta,5,5,5,4,5,5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/R.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,2,2,3,3,2,3 +locus_6sp_40.fasta,7,8,5,5,6,5 +locus_6sp_58.fasta,8,8,8,7,8,8 +locus_6sp_38.fasta,16,16,17,17,19,18 +locus_4sp_4.fasta,5,NaN,5,4,6,NaN +locus_4sp_6.fasta,10,9,8,9,NaN,NaN +locus_6sp_27.fasta,1,0,3,2,2,2 +locus_6sp_41.fasta,6,5,8,7,4,4 +locus_6sp_39.fasta,1,2,4,3,2,4 +locus_6sp_10.fasta,1,1,1,1,1,1 +locus_6sp_25.fasta,12,13,13,11,11,12 +locus_6sp_32.fasta,7,7,6,6,6,6 +locus_6sp_53.fasta,7,7,7,7,6,7 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,10,10,10,10,10,10 +locus_6sp_16.fasta,0,0,0,0,0,0 +locus_6sp_11.fasta,6,6,7,8,7,7 +locus_6sp_35.fasta,2,2,4,3,3,2 +locus_6sp_46.fasta,14,15,14,16,12,15 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,2 +locus_6sp_57.fasta,4,4,5,5,4,5 +locus_6sp_50.fasta,11,12,11,11,10,11
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/S.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,5,5,5,4,5,5 +locus_6sp_40.fasta,7,7,6,6,6,6 +locus_6sp_58.fasta,32,33,34,33,33,34 +locus_6sp_38.fasta,21,21,23,23,21,23 +locus_4sp_4.fasta,5,NaN,3,4,2,NaN +locus_4sp_6.fasta,2,1,1,2,NaN,NaN +locus_6sp_27.fasta,2,2,2,3,1,2 +locus_6sp_41.fasta,11,12,10,11,11,11 +locus_6sp_39.fasta,1,1,1,2,1,1 +locus_6sp_10.fasta,3,3,3,3,3,3 +locus_6sp_25.fasta,14,15,13,17,15,15 +locus_6sp_32.fasta,6,6,5,5,6,5 +locus_6sp_53.fasta,6,6,6,6,8,6 +locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN +locus_6sp_47.fasta,4,4,4,4,3,4 +locus_6sp_16.fasta,3,3,3,3,2,3 +locus_6sp_11.fasta,2,2,3,4,4,3 +locus_6sp_35.fasta,3,3,5,4,6,3 +locus_6sp_46.fasta,3,3,3,4,4,4 +locus_3sp_7.fasta,2,2,1,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,9,9,8,9,10,8 +locus_6sp_50.fasta,15,16,15,14,16,15
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/T.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,1,1,1,1,1,1 +locus_6sp_40.fasta,3,3,4,4,5,3 +locus_6sp_58.fasta,2,1,1,2,1,1 +locus_6sp_38.fasta,5,6,3,4,6,3 +locus_4sp_4.fasta,9,NaN,10,11,7,NaN +locus_4sp_6.fasta,4,4,4,4,NaN,NaN +locus_6sp_27.fasta,1,1,1,2,1,1 +locus_6sp_41.fasta,7,7,7,7,7,7 +locus_6sp_39.fasta,4,5,3,5,3,3 +locus_6sp_10.fasta,5,5,5,5,5,5 +locus_6sp_25.fasta,15,14,17,17,14,17 +locus_6sp_32.fasta,7,7,8,10,6,8 +locus_6sp_53.fasta,7,8,8,8,8,6 +locus_3sp_2.fasta,NaN,2,NaN,2,1,NaN +locus_6sp_47.fasta,4,3,4,4,4,4 +locus_6sp_16.fasta,2,2,2,2,2,3 +locus_6sp_11.fasta,5,5,4,4,7,5 +locus_6sp_35.fasta,5,5,3,4,5,4 +locus_6sp_46.fasta,5,5,2,3,4,3 +locus_3sp_7.fasta,0,0,1,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,7,7,7,7,6,6 +locus_6sp_50.fasta,12,12,12,11,9,12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/V.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,0,0,0,1,0 +locus_6sp_60.fasta,1,1,1,0,1,1 +locus_6sp_40.fasta,4,7,5,7,4,6 +locus_6sp_58.fasta,0,0,1,0,0,1 +locus_6sp_38.fasta,0,0,1,1,2,3 +locus_4sp_4.fasta,6,NaN,4,4,3,NaN +locus_4sp_6.fasta,2,2,2,3,NaN,NaN +locus_6sp_27.fasta,5,5,4,4,3,3 +locus_6sp_41.fasta,5,5,5,5,5,5 +locus_6sp_39.fasta,3,3,3,2,3,3 +locus_6sp_10.fasta,2,2,2,2,3,2 +locus_6sp_25.fasta,26,28,27,27,28,28 +locus_6sp_32.fasta,8,8,8,8,9,8 +locus_6sp_53.fasta,6,6,7,7,8,6 +locus_3sp_2.fasta,NaN,2,NaN,1,3,NaN +locus_6sp_47.fasta,5,5,5,5,5,5 +locus_6sp_16.fasta,4,5,4,3,2,4 +locus_6sp_11.fasta,10,10,9,11,8,9 +locus_6sp_35.fasta,10,9,10,10,8,9 +locus_6sp_46.fasta,4,5,7,6,5,5 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,10,10,10,10,10,10 +locus_6sp_50.fasta,21,23,20,23,23,19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/W.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,1,1,1,1,1,1 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,0,0 +locus_4sp_4.fasta,0,NaN,0,1,0,NaN +locus_4sp_6.fasta,5,5,5,5,NaN,NaN +locus_6sp_27.fasta,1,1,1,1,1,1 +locus_6sp_41.fasta,1,1,1,1,1,1 +locus_6sp_39.fasta,1,1,0,0,1,0 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,2,2,2,2,2,2 +locus_6sp_32.fasta,1,1,1,1,1,1 +locus_6sp_53.fasta,2,2,2,2,2,2 +locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,0,0,0,0,0,0 +locus_6sp_11.fasta,2,2,2,2,2,2 +locus_6sp_35.fasta,3,3,3,2,3,3 +locus_6sp_46.fasta,3,3,3,3,3,3 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,0,0,0,0,0,0 +locus_6sp_50.fasta,3,3,3,3,3,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/Y.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,2,2,2,2,2,2 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,12,12,12,12,11,12 +locus_4sp_4.fasta,2,NaN,3,2,2,NaN +locus_4sp_6.fasta,5,5,6,6,NaN,NaN +locus_6sp_27.fasta,0,0,0,0,1,0 +locus_6sp_41.fasta,0,0,0,0,0,0 +locus_6sp_39.fasta,3,2,2,2,2,2 +locus_6sp_10.fasta,6,6,6,6,5,6 +locus_6sp_25.fasta,12,12,12,13,13,12 +locus_6sp_32.fasta,5,5,4,4,5,5 +locus_6sp_53.fasta,4,4,4,4,4,4 +locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN +locus_6sp_47.fasta,2,2,2,2,2,2 +locus_6sp_16.fasta,1,1,2,2,1,2 +locus_6sp_11.fasta,1,1,1,2,1,1 +locus_6sp_35.fasta,2,2,3,3,2,2 +locus_6sp_46.fasta,2,2,2,2,2,2 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,3,3,2,2,3,2 +locus_6sp_50.fasta,14,14,14,13,13,14
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/AC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,2,2,2,2,2 +locus_6sp_60.fasta,3,3,3,3,3,3 +locus_6sp_40.fasta,8,7,8,6,8,8 +locus_6sp_58.fasta,1,1,0,0,1,0 +locus_6sp_38.fasta,4,4,5,4,2,3 +locus_4sp_4.fasta,6,NaN,7,6,7,NaN +locus_4sp_6.fasta,13,14,13,13,NaN,NaN +locus_6sp_41.fasta,7,7,7,7,8,7 +locus_6sp_27.fasta,2,3,3,2,2,2 +locus_6sp_39.fasta,3,3,4,3,3,4 +locus_6sp_10.fasta,8,8,8,8,7,8 +locus_6sp_25.fasta,20,19,21,18,20,19 +locus_6sp_32.fasta,9,9,11,9,9,11 +locus_6sp_53.fasta,7,6,6,6,6,8 +locus_3sp_2.fasta,NaN,3,NaN,3,4,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,5,4,4,4,5,4 +locus_6sp_11.fasta,16,16,14,15,15,15 +locus_6sp_35.fasta,8,8,6,7,6,7 +locus_6sp_46.fasta,7,7,7,6,5,8 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,10,10,9,8,9,10 +locus_6sp_50.fasta,38,37,38,40,39,39
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/APGC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,5,6,6,6,6,6 +locus_6sp_60.fasta,6,6,6,7,6,6 +locus_6sp_40.fasta,21,20,21,20,21,22 +locus_6sp_58.fasta,5,5,4,5,5,4 +locus_6sp_38.fasta,15,14,15,14,12,13 +locus_4sp_4.fasta,10,NaN,11,10,12,NaN +locus_4sp_6.fasta,23,24,23,23,NaN,NaN +locus_6sp_41.fasta,11,11,11,11,12,11 +locus_6sp_27.fasta,4,5,5,2,3,5 +locus_6sp_39.fasta,7,7,8,7,8,8 +locus_6sp_10.fasta,14,14,14,14,13,14 +locus_6sp_25.fasta,60,58,60,58,57,58 +locus_6sp_32.fasta,19,19,21,19,21,21 +locus_6sp_53.fasta,22,21,21,21,22,22 +locus_3sp_2.fasta,NaN,8,NaN,8,9,NaN +locus_6sp_47.fasta,8,8,8,8,9,8 +locus_6sp_16.fasta,11,10,10,10,11,10 +locus_6sp_11.fasta,37,37,35,34,36,36 +locus_6sp_35.fasta,17,17,14,17,14,16 +locus_6sp_46.fasta,13,13,13,11,10,13 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,20,20,19,18,19,20 +locus_6sp_50.fasta,90,89,90,92,92,91
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/AVLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,10,10,10,10,10,10 +locus_6sp_60.fasta,6,6,5,4,6,5 +locus_6sp_40.fasta,34,34,35,35,35,35 +locus_6sp_58.fasta,2,2,1,0,1,1 +locus_6sp_38.fasta,5,5,6,5,5,6 +locus_4sp_4.fasta,29,NaN,27,25,29,NaN +locus_4sp_6.fasta,14,16,15,15,NaN,NaN +locus_6sp_41.fasta,24,24,24,23,26,25 +locus_6sp_27.fasta,15,15,14,15,17,13 +locus_6sp_39.fasta,13,12,14,12,15,14 +locus_6sp_10.fasta,19,19,19,19,19,19 +locus_6sp_25.fasta,90,89,89,88,92,91 +locus_6sp_32.fasta,41,41,41,39,41,41 +locus_6sp_53.fasta,28,27,27,29,28,32 +locus_3sp_2.fasta,NaN,8,NaN,8,10,NaN +locus_6sp_47.fasta,15,16,15,15,15,15 +locus_6sp_16.fasta,14,14,13,13,13,13 +locus_6sp_11.fasta,51,51,50,51,46,50 +locus_6sp_35.fasta,26,26,28,27,25,25 +locus_6sp_46.fasta,39,39,40,39,37,39 +locus_3sp_7.fasta,12,12,12,NaN,NaN,NaN +locus_6sp_30.fasta,4,4,4,4,4,4 +locus_6sp_57.fasta,34,34,33,32,34,34 +locus_6sp_50.fasta,124,124,124,127,125,125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,12,12,12,12,12,12 +locus_6sp_60.fasta,9,9,8,7,9,8 +locus_6sp_40.fasta,39,39,40,40,40,40 +locus_6sp_58.fasta,2,2,1,0,1,1 +locus_6sp_38.fasta,18,18,19,18,18,19 +locus_4sp_4.fasta,36,NaN,36,35,38,NaN +locus_4sp_6.fasta,26,28,28,27,NaN,NaN +locus_6sp_41.fasta,29,29,29,29,32,31 +locus_6sp_27.fasta,19,19,16,17,21,16 +locus_6sp_39.fasta,22,21,22,20,22,22 +locus_6sp_10.fasta,35,35,35,35,35,35 +locus_6sp_25.fasta,119,118,118,119,122,121 +locus_6sp_32.fasta,55,55,55,53,56,56 +locus_6sp_53.fasta,45,44,44,45,45,47 +locus_3sp_2.fasta,NaN,13,NaN,13,15,NaN +locus_6sp_47.fasta,18,19,18,18,18,18 +locus_6sp_16.fasta,17,17,16,17,16,16 +locus_6sp_11.fasta,60,60,59,60,56,59 +locus_6sp_35.fasta,39,39,43,39,38,41 +locus_6sp_46.fasta,51,50,51,50,48,50 +locus_3sp_7.fasta,13,13,13,NaN,NaN,NaN +locus_6sp_30.fasta,7,7,7,7,7,7 +locus_6sp_57.fasta,38,38,37,36,38,38 +locus_6sp_50.fasta,150,150,151,152,150,151
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/DE.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,4,4,4,4,4,4 +locus_6sp_40.fasta,13,13,13,12,13,12 +locus_6sp_58.fasta,3,3,3,3,3,3 +locus_6sp_38.fasta,12,12,12,12,12,12 +locus_4sp_4.fasta,2,NaN,3,2,3,NaN +locus_4sp_6.fasta,14,14,14,14,NaN,NaN +locus_6sp_41.fasta,3,3,3,3,3,3 +locus_6sp_27.fasta,1,1,3,1,1,1 +locus_6sp_39.fasta,7,6,7,6,6,7 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,41,41,42,40,39,42 +locus_6sp_32.fasta,19,19,19,21,19,19 +locus_6sp_53.fasta,17,17,17,16,15,17 +locus_3sp_2.fasta,NaN,5,NaN,5,4,NaN +locus_6sp_47.fasta,6,6,6,6,6,6 +locus_6sp_16.fasta,9,9,8,8,11,8 +locus_6sp_11.fasta,22,22,22,22,21,21 +locus_6sp_35.fasta,2,2,2,2,2,2 +locus_6sp_46.fasta,26,26,27,26,26,26 +locus_3sp_7.fasta,7,7,7,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,4,3 +locus_6sp_57.fasta,12,12,12,12,12,12 +locus_6sp_50.fasta,11,11,10,11,11,10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,4,5,5,5,5,5 +locus_6sp_60.fasta,11,11,12,12,11,12 +locus_6sp_40.fasta,29,27,25,25,29,24 +locus_6sp_58.fasta,40,40,40,41,41,40 +locus_6sp_38.fasta,53,54,52,54,50,50 +locus_4sp_4.fasta,25,NaN,22,25,19,NaN +locus_4sp_6.fasta,25,25,21,24,NaN,NaN +locus_6sp_41.fasta,31,31,29,30,31,31 +locus_6sp_27.fasta,10,10,9,11,8,9 +locus_6sp_39.fasta,19,21,18,21,18,18 +locus_6sp_10.fasta,19,19,19,19,18,19 +locus_6sp_25.fasta,109,110,108,107,108,106 +locus_6sp_32.fasta,36,35,38,36,34,36 +locus_6sp_53.fasta,35,35,36,35,35,35 +locus_3sp_2.fasta,NaN,11,NaN,10,10,NaN +locus_6sp_47.fasta,20,19,20,20,19,20 +locus_6sp_16.fasta,14,13,15,13,15,15 +locus_6sp_11.fasta,45,45,44,44,48,45 +locus_6sp_35.fasta,17,17,16,16,20,16 +locus_6sp_46.fasta,28,27,24,28,29,28 +locus_3sp_7.fasta,17,18,17,NaN,NaN,NaN +locus_6sp_30.fasta,4,4,4,4,4,4 +locus_6sp_57.fasta,36,36,36,35,36,35 +locus_6sp_50.fasta,82,83,83,83,85,84
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/EK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,3,3,2,2,3,2 +locus_6sp_40.fasta,16,16,19,18,16,19 +locus_6sp_58.fasta,1,1,1,1,1,1 +locus_6sp_38.fasta,22,22,23,21,21,22 +locus_4sp_4.fasta,2,NaN,2,2,1,NaN +locus_4sp_6.fasta,12,12,16,13,NaN,NaN +locus_6sp_41.fasta,2,3,2,2,2,2 +locus_6sp_27.fasta,1,1,2,1,1,1 +locus_6sp_39.fasta,9,7,8,7,8,8 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,36,35,39,37,38,37 +locus_6sp_32.fasta,31,32,32,34,31,33 +locus_6sp_53.fasta,24,24,23,23,23,22 +locus_3sp_2.fasta,NaN,5,NaN,6,5,NaN +locus_6sp_47.fasta,12,12,12,12,12,12 +locus_6sp_16.fasta,8,8,7,8,8,7 +locus_6sp_11.fasta,29,29,28,29,28,28 +locus_6sp_35.fasta,3,3,3,3,3,3 +locus_6sp_46.fasta,45,46,49,44,48,47 +locus_3sp_7.fasta,7,6,7,NaN,NaN,NaN +locus_6sp_30.fasta,6,6,6,6,6,5 +locus_6sp_57.fasta,13,13,12,13,12,13 +locus_6sp_50.fasta,11,8,9,10,9,9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ERK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,4,4,2,3,4,2 +locus_6sp_40.fasta,25,24,29,28,25,29 +locus_6sp_58.fasta,2,2,2,2,2,2 +locus_6sp_38.fasta,37,37,38,36,36,37 +locus_4sp_4.fasta,3,NaN,3,3,1,NaN +locus_4sp_6.fasta,17,17,24,19,NaN,NaN +locus_6sp_41.fasta,3,5,3,3,3,3 +locus_6sp_27.fasta,2,2,2,2,1,2 +locus_6sp_39.fasta,13,10,11,10,12,11 +locus_6sp_10.fasta,6,6,6,6,6,6 +locus_6sp_25.fasta,54,52,59,57,59,56 +locus_6sp_32.fasta,50,52,51,53,50,52 +locus_6sp_53.fasta,35,35,33,33,34,32 +locus_3sp_2.fasta,NaN,9,NaN,10,9,NaN +locus_6sp_47.fasta,22,22,22,22,22,22 +locus_6sp_16.fasta,10,10,9,10,10,9 +locus_6sp_11.fasta,45,45,43,44,43,43 +locus_6sp_35.fasta,5,5,5,5,5,5 +locus_6sp_46.fasta,68,70,74,66,74,71 +locus_3sp_7.fasta,11,10,11,NaN,NaN,NaN +locus_6sp_30.fasta,10,10,10,10,9,8 +locus_6sp_57.fasta,18,18,17,18,17,18 +locus_6sp_50.fasta,18,13,15,16,15,15
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/FYMINK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,7,7,6,7,7,7 +locus_6sp_60.fasta,6,6,6,7,6,6 +locus_6sp_40.fasta,28,26,28,27,27,28 +locus_6sp_58.fasta,3,3,2,2,3,2 +locus_6sp_38.fasta,33,33,33,33,34,33 +locus_4sp_4.fasta,18,NaN,22,24,24,NaN +locus_4sp_6.fasta,26,26,28,25,NaN,NaN +locus_6sp_41.fasta,15,15,14,15,15,16 +locus_6sp_27.fasta,4,4,2,4,6,5 +locus_6sp_39.fasta,18,16,17,17,16,17 +locus_6sp_10.fasta,25,25,24,25,24,24 +locus_6sp_25.fasta,82,82,79,81,87,79 +locus_6sp_32.fasta,47,47,44,45,46,45 +locus_6sp_53.fasta,39,39,36,37,36,38 +locus_3sp_2.fasta,NaN,9,NaN,10,9,NaN +locus_6sp_47.fasta,16,17,16,16,16,16 +locus_6sp_16.fasta,8,8,9,11,9,8 +locus_6sp_11.fasta,45,45,47,45,45,46 +locus_6sp_35.fasta,20,21,21,22,23,23 +locus_6sp_46.fasta,49,49,49,46,51,48 +locus_3sp_7.fasta,8,8,8,NaN,NaN,NaN +locus_6sp_30.fasta,9,9,9,9,8,8 +locus_6sp_57.fasta,18,18,19,19,19,19 +locus_6sp_50.fasta,77,74,80,75,76,80
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/FYW.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,3,3,3,3,3,3 +locus_6sp_40.fasta,5,5,5,5,5,5 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,13,13,13,13,13,13 +locus_4sp_4.fasta,7,NaN,9,10,9,NaN +locus_4sp_6.fasta,12,12,13,12,NaN,NaN +locus_6sp_41.fasta,5,5,5,6,6,6 +locus_6sp_27.fasta,4,4,2,2,4,3 +locus_6sp_39.fasta,9,9,8,8,7,8 +locus_6sp_10.fasta,16,16,16,16,16,16 +locus_6sp_25.fasta,29,29,29,31,30,30 +locus_6sp_32.fasta,14,14,14,14,15,15 +locus_6sp_53.fasta,17,17,17,16,17,15 +locus_3sp_2.fasta,NaN,5,NaN,5,5,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,3,3,3,4,3,3 +locus_6sp_11.fasta,9,9,9,9,10,9 +locus_6sp_35.fasta,13,13,15,12,13,16 +locus_6sp_46.fasta,12,11,11,11,11,11 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,3,3 +locus_6sp_57.fasta,4,4,4,4,4,4 +locus_6sp_50.fasta,26,26,27,25,25,26
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/GARP.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,5,6,6,6,6,6 +locus_6sp_60.fasta,7,7,8,9,7,8 +locus_6sp_40.fasta,28,28,25,25,27,26 +locus_6sp_58.fasta,13,13,12,12,13,12 +locus_6sp_38.fasta,31,30,32,31,31,31 +locus_4sp_4.fasta,12,NaN,11,10,13,NaN +locus_4sp_6.fasta,20,20,18,19,NaN,NaN +locus_6sp_41.fasta,15,14,17,16,14,13 +locus_6sp_27.fasta,4,3,6,2,4,5 +locus_6sp_39.fasta,8,9,12,10,10,12 +locus_6sp_10.fasta,12,12,12,12,11,12 +locus_6sp_25.fasta,71,70,72,68,67,69 +locus_6sp_32.fasta,25,25,26,24,26,26 +locus_6sp_53.fasta,29,28,28,28,28,28 +locus_3sp_2.fasta,NaN,9,NaN,9,10,NaN +locus_6sp_47.fasta,18,18,18,18,19,18 +locus_6sp_16.fasta,10,9,9,9,10,9 +locus_6sp_11.fasta,41,41,40,40,41,41 +locus_6sp_35.fasta,14,14,16,16,14,14 +locus_6sp_46.fasta,27,28,27,27,22,28 +locus_3sp_7.fasta,4,4,4,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,3,4 +locus_6sp_57.fasta,23,23,23,22,22,24 +locus_6sp_50.fasta,98,98,98,100,99,99
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/IVYWREL.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,10,9,10,9,9,9 +locus_6sp_60.fasta,8,8,8,6,8,8 +locus_6sp_40.fasta,34,37,36,36,34,36 +locus_6sp_58.fasta,9,9,9,7,8,9 +locus_6sp_38.fasta,36,36,38,36,39,40 +locus_4sp_4.fasta,32,NaN,32,29,31,NaN +locus_4sp_6.fasta,39,39,40,40,NaN,NaN +locus_6sp_41.fasta,25,24,27,26,24,25 +locus_6sp_27.fasta,16,15,19,17,21,16 +locus_6sp_39.fasta,20,18,21,17,21,21 +locus_6sp_10.fasta,22,22,23,22,23,23 +locus_6sp_25.fasta,112,113,112,110,110,113 +locus_6sp_32.fasta,51,51,48,50,48,50 +locus_6sp_53.fasta,46,46,46,48,45,48 +locus_3sp_2.fasta,NaN,10,NaN,11,11,NaN +locus_6sp_47.fasta,29,29,29,29,29,29 +locus_6sp_16.fasta,17,18,17,18,16,17 +locus_6sp_11.fasta,53,54,55,58,52,54 +locus_6sp_35.fasta,30,30,33,32,30,28 +locus_6sp_46.fasta,69,70,74,72,68,71 +locus_3sp_7.fasta,14,13,14,NaN,NaN,NaN +locus_6sp_30.fasta,6,6,6,6,7,7 +locus_6sp_57.fasta,36,36,35,36,36,36 +locus_6sp_50.fasta,103,104,101,101,98,100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/QH.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,4,4,4,4,4,4 +locus_6sp_58.fasta,1,1,1,2,1,1 +locus_6sp_38.fasta,13,13,12,12,10,11 +locus_4sp_4.fasta,6,NaN,4,4,5,NaN +locus_4sp_6.fasta,6,7,6,7,NaN,NaN +locus_6sp_41.fasta,3,3,3,3,3,3 +locus_6sp_27.fasta,5,5,4,5,5,5 +locus_6sp_39.fasta,7,8,6,7,7,6 +locus_6sp_10.fasta,3,3,3,3,3,3 +locus_6sp_25.fasta,21,21,21,20,21,19 +locus_6sp_32.fasta,5,4,6,4,4,5 +locus_6sp_53.fasta,7,7,8,8,7,6 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,6,6,6,6,6,6 +locus_6sp_16.fasta,2,2,3,2,2,3 +locus_6sp_11.fasta,9,9,9,8,8,9 +locus_6sp_35.fasta,2,2,2,2,2,3 +locus_6sp_46.fasta,6,5,6,8,8,7 +locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,5,5,5,5,5,5 +locus_6sp_50.fasta,7,7,7,7,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/RHK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,3,3,3,4,3,3 +locus_6sp_40.fasta,18,18,17,18,17,18 +locus_6sp_58.fasta,10,10,10,10,10,10 +locus_6sp_38.fasta,42,42,42,42,42,43 +locus_4sp_4.fasta,12,NaN,10,9,11,NaN +locus_4sp_6.fasta,17,17,18,18,NaN,NaN +locus_6sp_41.fasta,8,8,10,9,5,6 +locus_6sp_27.fasta,5,4,6,6,4,6 +locus_6sp_39.fasta,9,9,11,10,9,11 +locus_6sp_10.fasta,5,5,5,5,5,5 +locus_6sp_25.fasta,40,40,44,41,42,42 +locus_6sp_32.fasta,27,28,27,27,26,26 +locus_6sp_53.fasta,21,21,22,20,20,18 +locus_3sp_2.fasta,NaN,5,NaN,5,5,NaN +locus_6sp_47.fasta,23,23,23,23,23,23 +locus_6sp_16.fasta,3,3,3,3,3,3 +locus_6sp_11.fasta,22,23,23,24,23,22 +locus_6sp_35.fasta,6,6,8,7,7,7 +locus_6sp_46.fasta,37,39,39,38,38,39 +locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN +locus_6sp_30.fasta,5,5,5,5,4,5 +locus_6sp_57.fasta,11,11,12,12,11,12 +locus_6sp_50.fasta,20,19,19,20,19,19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/RHKDE.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,3,3,3,3 +locus_6sp_60.fasta,7,7,7,8,7,7 +locus_6sp_40.fasta,31,31,30,30,30,30 +locus_6sp_58.fasta,13,13,13,13,13,13 +locus_6sp_38.fasta,54,54,54,54,54,55 +locus_4sp_4.fasta,14,NaN,13,11,14,NaN +locus_4sp_6.fasta,31,31,32,32,NaN,NaN +locus_6sp_41.fasta,11,11,13,12,8,9 +locus_6sp_27.fasta,6,5,9,7,5,7 +locus_6sp_39.fasta,16,15,18,16,15,18 +locus_6sp_10.fasta,9,9,9,9,9,9 +locus_6sp_25.fasta,81,81,86,81,81,84 +locus_6sp_32.fasta,46,47,46,48,45,45 +locus_6sp_53.fasta,38,38,39,36,35,35 +locus_3sp_2.fasta,NaN,10,NaN,10,9,NaN +locus_6sp_47.fasta,29,29,29,29,29,29 +locus_6sp_16.fasta,12,12,11,11,14,11 +locus_6sp_11.fasta,44,45,45,46,44,43 +locus_6sp_35.fasta,8,8,10,9,9,9 +locus_6sp_46.fasta,63,65,66,64,64,65 +locus_3sp_7.fasta,12,12,12,NaN,NaN,NaN +locus_6sp_30.fasta,8,8,8,8,8,8 +locus_6sp_57.fasta,23,23,24,24,23,24 +locus_6sp_50.fasta,31,30,29,31,30,29
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/STNQ.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,7,7,8,7,7,8 +locus_6sp_40.fasta,13,13,12,12,13,11 +locus_6sp_58.fasta,35,35,36,36,36,36 +locus_6sp_38.fasta,33,34,33,34,34,32 +locus_4sp_4.fasta,15,NaN,14,18,10,NaN +locus_4sp_6.fasta,16,14,13,14,NaN,NaN +locus_6sp_41.fasta,23,23,21,22,23,23 +locus_6sp_27.fasta,5,5,4,7,5,5 +locus_6sp_39.fasta,10,12,8,12,10,8 +locus_6sp_10.fasta,10,10,10,10,10,10 +locus_6sp_25.fasta,57,59,54,57,57,53 +locus_6sp_32.fasta,20,19,20,20,18,20 +locus_6sp_53.fasta,21,22,21,23,23,22 +locus_3sp_2.fasta,NaN,4,NaN,4,3,NaN +locus_6sp_47.fasta,12,11,12,12,11,12 +locus_6sp_16.fasta,6,6,8,7,5,8 +locus_6sp_11.fasta,22,21,22,22,26,24 +locus_6sp_35.fasta,11,11,9,10,14,9 +locus_6sp_46.fasta,17,16,14,18,20,17 +locus_3sp_7.fasta,10,10,10,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,21,21,21,22,21,20 +locus_6sp_50.fasta,38,39,39,36,38,39
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/VLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,9,8,8,8,8,8 +locus_6sp_60.fasta,4,4,3,2,4,3 +locus_6sp_40.fasta,26,27,28,29,27,28 +locus_6sp_58.fasta,1,1,1,0,0,1 +locus_6sp_38.fasta,1,1,1,1,3,3 +locus_4sp_4.fasta,26,NaN,25,23,27,NaN +locus_4sp_6.fasta,14,15,15,15,NaN,NaN +locus_6sp_41.fasta,19,19,19,18,20,20 +locus_6sp_27.fasta,14,14,13,15,16,13 +locus_6sp_39.fasta,10,9,10,9,12,10 +locus_6sp_10.fasta,14,14,14,14,15,14 +locus_6sp_25.fasta,71,71,69,71,73,73 +locus_6sp_32.fasta,33,33,31,31,33,31 +locus_6sp_53.fasta,21,21,21,23,22,25 +locus_3sp_2.fasta,NaN,5,NaN,5,6,NaN +locus_6sp_47.fasta,14,15,14,14,14,14 +locus_6sp_16.fasta,10,11,10,10,9,10 +locus_6sp_11.fasta,37,37,38,38,33,37 +locus_6sp_35.fasta,23,23,24,24,22,22 +locus_6sp_46.fasta,32,32,33,33,32,31 +locus_3sp_7.fasta,9,9,9,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,3,3 +locus_6sp_57.fasta,25,25,25,25,26,25 +locus_6sp_50.fasta,89,90,89,90,89,89
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.111111111111,0.25,0.25,0.25,0.25,0.25 +locus_6sp_60.fasta,0.75,0.75,1.0,1.5,0.75,1.0 +locus_6sp_40.fasta,0.307692307692,0.259259259259,0.285714285714,0.206896551724,0.296296296296,0.285714285714 +locus_6sp_58.fasta,1.0,1.0,0.0,-1,-1,0.0 +locus_6sp_38.fasta,4.0,4.0,5.0,4.0,0.666666666667,1.0 +locus_4sp_4.fasta,0.230769230769,NaN,0.28,0.260869565217,0.259259259259,NaN +locus_4sp_6.fasta,0.928571428571,0.933333333333,0.866666666667,0.866666666667,NaN,NaN +locus_6sp_41.fasta,0.368421052632,0.368421052632,0.368421052632,0.388888888889,0.4,0.35 +locus_6sp_27.fasta,0.142857142857,0.214285714286,0.230769230769,0.133333333333,0.125,0.153846153846 +locus_6sp_39.fasta,0.3,0.333333333333,0.4,0.333333333333,0.25,0.4 +locus_6sp_10.fasta,0.571428571429,0.571428571429,0.571428571429,0.571428571429,0.466666666667,0.571428571429 +locus_6sp_25.fasta,0.281690140845,0.267605633803,0.304347826087,0.253521126761,0.27397260274,0.260273972603 +locus_6sp_32.fasta,0.272727272727,0.272727272727,0.354838709677,0.290322580645,0.272727272727,0.354838709677 +locus_6sp_53.fasta,0.333333333333,0.285714285714,0.285714285714,0.260869565217,0.272727272727,0.32 +locus_3sp_2.fasta,NaN,0.6,NaN,0.6,0.666666666667,NaN +locus_6sp_47.fasta,0.0714285714286,0.0666666666667,0.0714285714286,0.0714285714286,0.0714285714286,0.0714285714286 +locus_6sp_16.fasta,0.5,0.363636363636,0.4,0.4,0.555555555556,0.4 +locus_6sp_11.fasta,0.432432432432,0.432432432432,0.368421052632,0.394736842105,0.454545454545,0.405405405405 +locus_6sp_35.fasta,0.347826086957,0.347826086957,0.25,0.291666666667,0.272727272727,0.318181818182 +locus_6sp_46.fasta,0.21875,0.21875,0.212121212121,0.181818181818,0.15625,0.258064516129 +locus_3sp_7.fasta,0.333333333333,0.333333333333,0.333333333333,NaN,NaN,NaN +locus_6sp_30.fasta,0.333333333333,0.333333333333,0.333333333333,0.333333333333,0.333333333333,0.333333333333 +locus_6sp_57.fasta,0.4,0.4,0.36,0.32,0.346153846154,0.4 +locus_6sp_50.fasta,0.426966292135,0.411111111111,0.426966292135,0.444444444444,0.438202247191,0.438202247191
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.555555555556,0.75,0.75,0.75,0.75,0.75 +locus_6sp_60.fasta,1.5,1.5,2.0,3.5,1.5,2.0 +locus_6sp_40.fasta,0.807692307692,0.740740740741,0.75,0.689655172414,0.777777777778,0.785714285714 +locus_6sp_58.fasta,5.0,5.0,4.0,-1,-1,4.0 +locus_6sp_38.fasta,15.0,14.0,15.0,14.0,4.0,4.33333333333 +locus_4sp_4.fasta,0.384615384615,NaN,0.44,0.434782608696,0.444444444444,NaN +locus_4sp_6.fasta,1.64285714286,1.6,1.53333333333,1.53333333333,NaN,NaN +locus_6sp_41.fasta,0.578947368421,0.578947368421,0.578947368421,0.611111111111,0.6,0.55 +locus_6sp_27.fasta,0.285714285714,0.357142857143,0.384615384615,0.133333333333,0.1875,0.384615384615 +locus_6sp_39.fasta,0.7,0.777777777778,0.8,0.777777777778,0.666666666667,0.8 +locus_6sp_10.fasta,1.0,1.0,1.0,1.0,0.866666666667,1.0 +locus_6sp_25.fasta,0.845070422535,0.816901408451,0.869565217391,0.816901408451,0.780821917808,0.794520547945 +locus_6sp_32.fasta,0.575757575758,0.575757575758,0.677419354839,0.612903225806,0.636363636364,0.677419354839 +locus_6sp_53.fasta,1.04761904762,1.0,1.0,0.913043478261,1.0,0.88 +locus_3sp_2.fasta,NaN,1.6,NaN,1.6,1.5,NaN +locus_6sp_47.fasta,0.571428571429,0.533333333333,0.571428571429,0.571428571429,0.642857142857,0.571428571429 +locus_6sp_16.fasta,1.1,0.909090909091,1.0,1.0,1.22222222222,1.0 +locus_6sp_11.fasta,1.0,1.0,0.921052631579,0.894736842105,1.09090909091,0.972972972973 +locus_6sp_35.fasta,0.739130434783,0.739130434783,0.583333333333,0.708333333333,0.636363636364,0.727272727273 +locus_6sp_46.fasta,0.40625,0.40625,0.393939393939,0.333333333333,0.3125,0.41935483871 +locus_3sp_7.fasta,0.333333333333,0.333333333333,0.333333333333,NaN,NaN,NaN +locus_6sp_30.fasta,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.666666666667 +locus_6sp_57.fasta,0.8,0.8,0.76,0.72,0.730769230769,0.8 +locus_6sp_50.fasta,1.01123595506,0.988888888889,1.01123595506,1.02222222222,1.03370786517,1.02247191011
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2.0,2.0,2.0,2.0,2.0,2.0 +locus_6sp_60.fasta,-1,-1,-1,-1,-1,-1 +locus_6sp_40.fasta,4.0,4.0,4.75,4.5,4.0,4.75 +locus_6sp_58.fasta,1.0,1.0,1.0,0.5,1.0,1.0 +locus_6sp_38.fasta,1.69230769231,1.69230769231,1.91666666667,1.75,2.1,2.0 +locus_4sp_4.fasta,0.333333333333,NaN,0.5,0.5,0.2,NaN +locus_4sp_6.fasta,2.0,1.71428571429,2.66666666667,1.85714285714,NaN,NaN +locus_6sp_41.fasta,0.666666666667,1.0,0.666666666667,0.666666666667,0.666666666667,0.666666666667 +locus_6sp_27.fasta,0.2,0.2,0.5,0.2,0.2,0.2 +locus_6sp_39.fasta,1.28571428571,0.875,1.33333333333,1.0,1.14285714286,1.33333333333 +locus_6sp_10.fasta,1.33333333333,1.33333333333,1.33333333333,1.33333333333,1.33333333333,1.33333333333 +locus_6sp_25.fasta,1.71428571429,1.66666666667,1.85714285714,1.85,1.80952380952,1.94736842105 +locus_6sp_32.fasta,6.2,8.0,5.33333333333,8.5,7.75,6.6 +locus_6sp_53.fasta,3.42857142857,3.42857142857,2.875,2.875,3.28571428571,3.66666666667 +locus_3sp_2.fasta,NaN,5.0,NaN,6.0,5.0,NaN +locus_6sp_47.fasta,2.0,2.0,2.0,2.0,2.0,2.0 +locus_6sp_16.fasta,4.0,4.0,2.33333333333,4.0,4.0,2.33333333333 +locus_6sp_11.fasta,3.22222222222,3.22222222222,3.11111111111,3.625,3.5,3.11111111111 +locus_6sp_35.fasta,1.5,1.5,1.5,1.5,1.5,1.0 +locus_6sp_46.fasta,7.5,9.2,8.16666666667,5.5,6.0,6.71428571429 +locus_3sp_7.fasta,1.4,1.2,1.4,NaN,NaN,NaN +locus_6sp_30.fasta,-1,-1,-1,-1,-1,-1 +locus_6sp_57.fasta,2.6,2.6,2.4,2.6,2.4,2.6 +locus_6sp_50.fasta,1.57142857143,1.14285714286,1.28571428571,1.42857142857,1.125,1.28571428571
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.5,0.4,0.4,0.4,0.4,0.4 +locus_6sp_60.fasta,0.363636363636,0.363636363636,0.166666666667,0.25,0.363636363636,0.166666666667 +locus_6sp_40.fasta,0.862068965517,0.888888888889,1.16,1.12,0.862068965517,1.20833333333 +locus_6sp_58.fasta,0.05,0.05,0.05,0.0487804878049,0.0487804878049,0.05 +locus_6sp_38.fasta,0.698113207547,0.685185185185,0.730769230769,0.666666666667,0.72,0.74 +locus_4sp_4.fasta,0.12,NaN,0.136363636364,0.12,0.0526315789474,NaN +locus_4sp_6.fasta,0.68,0.68,1.14285714286,0.791666666667,NaN,NaN +locus_6sp_41.fasta,0.0967741935484,0.161290322581,0.103448275862,0.1,0.0967741935484,0.0967741935484 +locus_6sp_27.fasta,0.2,0.2,0.222222222222,0.181818181818,0.125,0.222222222222 +locus_6sp_39.fasta,0.684210526316,0.47619047619,0.611111111111,0.47619047619,0.666666666667,0.611111111111 +locus_6sp_10.fasta,0.315789473684,0.315789473684,0.315789473684,0.315789473684,0.333333333333,0.315789473684 +locus_6sp_25.fasta,0.495412844037,0.472727272727,0.546296296296,0.532710280374,0.546296296296,0.528301886792 +locus_6sp_32.fasta,1.38888888889,1.48571428571,1.34210526316,1.47222222222,1.47058823529,1.44444444444 +locus_6sp_53.fasta,1.0,1.0,0.916666666667,0.942857142857,0.971428571429,0.914285714286 +locus_3sp_2.fasta,NaN,0.818181818182,NaN,1.0,0.9,NaN +locus_6sp_47.fasta,1.1,1.15789473684,1.1,1.1,1.15789473684,1.1 +locus_6sp_16.fasta,0.714285714286,0.769230769231,0.6,0.769230769231,0.666666666667,0.6 +locus_6sp_11.fasta,1.0,1.0,0.977272727273,1.0,0.895833333333,0.955555555556 +locus_6sp_35.fasta,0.294117647059,0.294117647059,0.3125,0.3125,0.25,0.3125 +locus_6sp_46.fasta,2.42857142857,2.59259259259,3.08333333333,2.35714285714,2.55172413793,2.53571428571 +locus_3sp_7.fasta,0.647058823529,0.555555555556,0.647058823529,NaN,NaN,NaN +locus_6sp_30.fasta,2.5,2.5,2.5,2.5,2.25,2.0 +locus_6sp_57.fasta,0.5,0.5,0.472222222222,0.514285714286,0.472222222222,0.514285714286 +locus_6sp_50.fasta,0.219512195122,0.156626506024,0.180722891566,0.192771084337,0.176470588235,0.178571428571
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.285714285714,0.285714285714,0.333333333333,0.285714285714,0.285714285714,0.285714285714 +locus_6sp_60.fasta,0.5,0.5,0.333333333333,0.285714285714,0.5,0.333333333333 +locus_6sp_40.fasta,0.571428571429,0.615384615385,0.678571428571,0.666666666667,0.592592592593,0.678571428571 +locus_6sp_58.fasta,0.333333333333,0.333333333333,0.5,0.5,0.333333333333,0.5 +locus_6sp_38.fasta,0.666666666667,0.666666666667,0.69696969697,0.636363636364,0.617647058824,0.666666666667 +locus_4sp_4.fasta,0.111111111111,NaN,0.0909090909091,0.0833333333333,0.0416666666667,NaN +locus_4sp_6.fasta,0.461538461538,0.461538461538,0.571428571429,0.52,NaN,NaN +locus_6sp_41.fasta,0.133333333333,0.2,0.142857142857,0.133333333333,0.133333333333,0.125 +locus_6sp_27.fasta,0.25,0.25,1.0,0.25,0.166666666667,0.2 +locus_6sp_39.fasta,0.5,0.4375,0.470588235294,0.411764705882,0.5,0.470588235294 +locus_6sp_10.fasta,0.16,0.16,0.166666666667,0.16,0.166666666667,0.166666666667 +locus_6sp_25.fasta,0.439024390244,0.426829268293,0.493670886076,0.456790123457,0.436781609195,0.46835443038 +locus_6sp_32.fasta,0.659574468085,0.68085106383,0.727272727273,0.755555555556,0.673913043478,0.733333333333 +locus_6sp_53.fasta,0.615384615385,0.615384615385,0.638888888889,0.621621621622,0.638888888889,0.578947368421 +locus_3sp_2.fasta,NaN,0.555555555556,NaN,0.6,0.555555555556,NaN +locus_6sp_47.fasta,0.75,0.705882352941,0.75,0.75,0.75,0.75 +locus_6sp_16.fasta,1.0,1.0,0.777777777778,0.727272727273,0.888888888889,0.875 +locus_6sp_11.fasta,0.644444444444,0.644444444444,0.595744680851,0.644444444444,0.622222222222,0.608695652174 +locus_6sp_35.fasta,0.15,0.142857142857,0.142857142857,0.136363636364,0.130434782609,0.130434782609 +locus_6sp_46.fasta,0.918367346939,0.938775510204,1.0,0.95652173913,0.941176470588,0.979166666667 +locus_3sp_7.fasta,0.875,0.75,0.875,NaN,NaN,NaN +locus_6sp_30.fasta,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.75,0.625 +locus_6sp_57.fasta,0.722222222222,0.722222222222,0.631578947368,0.684210526316,0.631578947368,0.684210526316 +locus_6sp_50.fasta,0.142857142857,0.108108108108,0.1125,0.133333333333,0.118421052632,0.1125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_hydration.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,45.0,45.0,45.0,45.0,45.0,45.0 +locus_6sp_60.fasta,61.5,61.5,61.0,62.0,61.5,61.0 +locus_6sp_40.fasta,247.0,247.0,246.5,245.0,245.0,245.5 +locus_6sp_58.fasta,126.5,126.5,127.5,130.5,127.5,127.5 +locus_6sp_38.fasta,376.0,375.0,374.5,372.5,367.5,374.0 +locus_4sp_4.fasta,135.0,NaN,134.0,129.0,130.5,NaN +locus_4sp_6.fasta,257.0,256.0,264.0,262.5,NaN,NaN +locus_6sp_41.fasta,126.0,127.5,128.0,126.0,118.0,121.0 +locus_6sp_27.fasta,57.5,55.5,74.0,61.5,55.5,62.5 +locus_6sp_39.fasta,138.5,129.5,135.0,130.5,130.0,135.0 +locus_6sp_10.fasta,125.0,125.0,125.0,125.0,122.0,125.0 +locus_6sp_25.fasta,747.0,745.5,758.5,744.5,742.0,749.5 +locus_6sp_32.fasta,359.5,362.0,359.0,372.0,356.5,359.5 +locus_6sp_53.fasta,317.0,318.0,319.5,311.5,305.5,307.0 +locus_3sp_2.fasta,NaN,85.5,NaN,87.0,79.5,NaN +locus_6sp_47.fasta,180.0,179.0,180.0,180.0,179.0,180.0 +locus_6sp_16.fasta,114.0,114.0,112.5,112.0,123.0,112.5 +locus_6sp_11.fasta,378.5,380.5,380.0,384.5,378.0,374.0 +locus_6sp_35.fasta,118.5,118.5,119.5,121.5,121.5,114.5 +locus_6sp_46.fasta,429.5,435.0,442.5,432.0,440.0,437.5 +locus_3sp_7.fasta,102.5,101.0,102.5,NaN,NaN,NaN +locus_6sp_30.fasta,57.0,57.0,57.0,57.0,60.0,55.5 +locus_6sp_57.fasta,226.5,226.5,224.0,226.5,225.0,224.5 +locus_6sp_50.fasta,473.5,468.0,463.5,469.0,467.5,464.5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,15.64,15.52,15.67,15.52,15.48,15.52 +locus_6sp_60.fasta,19.64,19.64,19.24,19.04,19.64,19.24 +locus_6sp_40.fasta,71.19,71.17,71.58,71.77,71.43,71.62 +locus_6sp_58.fasta,38.79,38.83,38.79,38.62,38.55,38.79 +locus_6sp_38.fasta,81.92,81.86,82.03,81.87,82.29,82.24 +locus_4sp_4.fasta,55.12,NaN,54.64,54.51,54.66,NaN +locus_4sp_6.fasta,67.26,67.51,67.91,67.51,NaN,NaN +locus_6sp_41.fasta,51.81,52.05,51.85,51.91,52.2,52.23 +locus_6sp_27.fasta,25.85,25.76,25.41,25.71,26.01,25.59 +locus_6sp_39.fasta,38.27,38.12,38.34,38.04,38.67,38.34 +locus_6sp_10.fasta,45.83,45.83,45.98,45.83,46.26,45.98 +locus_6sp_25.fasta,219.26,218.84,219.08,219.6,219.52,219.72 +locus_6sp_32.fasta,98.84,98.99,98.67,98.57,98.6,98.67 +locus_6sp_53.fasta,87.81,87.77,87.58,88.01,88.13,87.94 +locus_3sp_2.fasta,NaN,23.01,NaN,23.11,23.31,NaN +locus_6sp_47.fasta,48.9,48.95,48.9,48.9,48.8,48.9 +locus_6sp_16.fasta,30.88,31.0,30.61,30.81,30.52,30.69 +locus_6sp_11.fasta,110.48,110.63,110.48,110.41,110.02,110.42 +locus_6sp_35.fasta,54.48,54.52,55.0,54.63,54.6,54.4 +locus_6sp_46.fasta,103.31,103.35,103.88,103.24,103.59,103.44 +locus_3sp_7.fasta,25.94,25.88,25.9,NaN,NaN,NaN +locus_6sp_30.fasta,13.25,13.25,13.25,13.25,13.09,13.13 +locus_6sp_57.fasta,68.74,68.74,68.68,68.74,68.88,68.78 +locus_6sp_50.fasta,205.01,204.83,204.81,204.76,204.37,204.67
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2202.0,2164.0,2164.0,2164.0,2145.0,2164.0 +locus_6sp_60.fasta,2631.0,2631.0,2616.0,2603.0,2631.0,2616.0 +locus_6sp_40.fasta,10101.0,10132.0,10106.0,10120.0,10094.0,10093.0 +locus_6sp_58.fasta,4711.0,4691.0,4678.0,4653.0,4663.0,4678.0 +locus_6sp_38.fasta,12698.0,12701.0,12664.0,12654.0,12843.0,12756.0 +locus_4sp_4.fasta,7925.0,NaN,8022.0,7964.0,8152.0,NaN +locus_4sp_6.fasta,10595.0,10587.0,10722.0,10619.0,NaN,NaN +locus_6sp_41.fasta,7107.0,7071.0,7234.0,7170.0,7037.0,7070.0 +locus_6sp_27.fasta,3695.0,3633.0,3713.0,3763.0,3851.0,3731.0 +locus_6sp_39.fasta,5787.0,5768.0,5787.0,5731.0,5749.0,5787.0 +locus_6sp_10.fasta,6919.0,6919.0,6919.0,6919.0,6951.0,6919.0 +locus_6sp_25.fasta,31048.0,31038.0,31072.0,31049.0,31208.0,31071.0 +locus_6sp_32.fasta,14655.0,14676.0,14543.0,14585.0,14554.0,14584.0 +locus_6sp_53.fasta,12891.0,12917.0,12885.0,12899.0,12753.0,12841.0 +locus_3sp_2.fasta,NaN,3365.0,NaN,3402.0,3353.0,NaN +locus_6sp_47.fasta,7357.0,7388.0,7357.0,7357.0,7332.0,7357.0 +locus_6sp_16.fasta,4093.0,4131.0,4133.0,4191.0,4116.0,4130.0 +locus_6sp_11.fasta,15542.0,15546.0,15644.0,15666.0,15488.0,15585.0 +locus_6sp_35.fasta,7718.0,7737.0,7901.0,7679.0,7737.0,7819.0 +locus_6sp_46.fasta,16044.0,16059.0,16094.0,16156.0,16121.0,16087.0 +locus_3sp_7.fasta,3822.0,3804.0,3842.0,NaN,NaN,NaN +locus_6sp_30.fasta,2160.0,2160.0,2160.0,2160.0,2134.0,2173.0 +locus_6sp_57.fasta,9302.0,9302.0,9382.0,9406.0,9321.0,9374.0 +locus_6sp_50.fasta,27199.0,27151.0,27205.0,27077.0,26938.0,27156.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2320.97,2292.91,2274.88,2292.91,2278.88,2292.91 +locus_6sp_60.fasta,2875.44,2875.44,2904.37,2890.36,2875.44,2904.37 +locus_6sp_40.fasta,10730.6,10772.64,10677.71,10681.73,10687.63,10669.73 +locus_6sp_58.fasta,5382.96,5368.93,5370.9,5363.87,5369.85,5370.9 +locus_6sp_38.fasta,14051.67,14055.66,14016.61,14018.58,14138.94,14087.76 +locus_4sp_4.fasta,8273.9,NaN,8399.0,8384.92,8550.4,NaN +locus_4sp_6.fasta,11670.96,11635.0,11719.17,11667.99,NaN,NaN +locus_6sp_41.fasta,7552.64,7497.62,7665.85,7611.72,7445.58,7480.58 +locus_6sp_27.fasta,3817.14,3763.09,3880.11,3891.27,3935.29,3871.22 +locus_6sp_39.fasta,6222.42,6222.47,6204.5,6184.45,6113.49,6204.5 +locus_6sp_10.fasta,7526.22,7526.22,7508.19,7526.22,7520.32,7508.19 +locus_6sp_25.fasta,33249.0,33294.9,33269.07,33233.11,33387.33,33234.18 +locus_6sp_32.fasta,15445.36,15446.41,15354.27,15414.27,15382.32,15393.26 +locus_6sp_53.fasta,13805.76,13835.79,13840.75,13785.8,13638.67,13709.73 +locus_3sp_2.fasta,NaN,3643.31,NaN,3671.37,3598.35,NaN +locus_6sp_47.fasta,7739.7,7769.79,7739.7,7739.7,7709.68,7739.7 +locus_6sp_16.fasta,4402.26,4430.32,4461.23,4508.34,4458.21,4448.25 +locus_6sp_11.fasta,16434.68,16426.67,16557.81,16592.75,16450.49,16492.74 +locus_6sp_35.fasta,8146.67,8160.7,8310.84,8072.54,8176.59,8286.85 +locus_6sp_46.fasta,16798.11,16795.14,16783.11,16934.22,16849.13,16833.11 +locus_3sp_7.fasta,4052.77,4038.74,4066.8,NaN,NaN,NaN +locus_6sp_30.fasta,2321.9,2321.9,2321.9,2321.9,2320.82,2349.91 +locus_6sp_57.fasta,9928.19,9928.19,10011.35,10041.38,9942.22,9995.35 +locus_6sp_50.fasta,28621.97,28607.88,28658.02,28528.93,28444.68,28613.98
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/A.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,1,4,5 +"Lower",1,4,4,0 +"Difference",2,-3,0,5 +"Trial_Number",4,5,8,5 +"p-value",0.625,0.375,1,0.0625 +"probability_of_success",0.75,0.2,0.5,1 +"confidence_interval_low",0.194120449683243,0.00505076337946806,0.157012770487058,0.478176249895019 +"confidence_interval_high",0.99369053679029,0.716417936118089,0.842987229512942,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/C.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,0,0,2 +"Lower",0,0,2,0 +"Difference",1,0,-2,2 +"Trial_Number",1,0,2,2 +"p-value",1,NA,0.5,0.5 +"probability_of_success",1,NA,0,1 +"confidence_interval_low",0.025,NA,0,0.158113883008419 +"confidence_interval_high",1,NA,0.841886116991581,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/D.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,2,4,2 +"Lower",1,2,3,4 +"Difference",1,0,1,-2 +"Trial_Number",3,4,7,6 +"p-value",1,1,1,0.6875 +"probability_of_success",0.666666666666667,0.5,0.571428571428571,0.333333333333333 +"confidence_interval_low",0.0942993240502461,0.067585986488543,0.184051567640083,0.0432718682927417 +"confidence_interval_high",0.991596241340387,0.932414013511457,0.901011721557492,0.777221904496488
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/E.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,3,2,5 +"Lower",0,3,4,1 +"Difference",2,0,-2,4 +"Trial_Number",2,6,6,6 +"p-value",0.5,1,0.6875,0.21875 +"probability_of_success",1,0.5,0.333333333333333,0.833333333333333 +"confidence_interval_low",0.158113883008419,0.118117248757025,0.0432718682927417,0.358765421002325 +"confidence_interval_high",1,0.881882751242975,0.777221904496488,0.995789255485511
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/F.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,0,3,1 +"Lower",2,3,1,2 +"Difference",-1,-3,2,-1 +"Trial_Number",3,3,4,3 +"p-value",1,0.25,0.625,1 +"probability_of_success",0.333333333333333,0,0.75,0.333333333333333 +"confidence_interval_low",0.00840375865961264,0,0.194120449683243,0.00840375865961264 +"confidence_interval_high",0.905700675949754,0.707598226178713,0.99369053679029,0.905700675949754
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/G.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,5,0 +"Lower",0,2,1,0 +"Difference",1,-1,4,0 +"Trial_Number",1,3,6,0 +"p-value",1,1,0.21875,NA +"probability_of_success",1,0.333333333333333,0.833333333333333,NA +"confidence_interval_low",0.025,0.00840375865961264,0.358765421002325,NA +"confidence_interval_high",1,0.905700675949754,0.995789255485511,NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/H.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,3,1,2 +"Lower",1,0,4,3 +"Difference",0,3,-3,-1 +"Trial_Number",2,3,5,5 +"p-value",1,0.25,0.375,1 +"probability_of_success",0.5,1,0.2,0.4 +"confidence_interval_low",0.0125791170934251,0.292401773821287,0.00505076337946806,0.0527449505263169 +"confidence_interval_high",0.987420882906575,1,0.716417936118089,0.853367200365327
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/I.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,2,6,2 +"Lower",3,4,4,2 +"Difference",2,-2,2,0 +"Trial_Number",8,6,10,4 +"p-value",0.7265625,0.6875,0.75390625,1 +"probability_of_success",0.625,0.333333333333333,0.6,0.5 +"confidence_interval_low",0.244863216366552,0.0432718682927417,0.262378076606945,0.067585986488543 +"confidence_interval_high",0.914766585862746,0.777221904496488,0.878447741880173,0.932414013511457
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/K.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,1,3,0 +"Lower",3,1,1,2 +"Difference",0,0,2,-2 +"Trial_Number",6,2,4,2 +"p-value",1,1,0.625,0.5 +"probability_of_success",0.5,0.5,0.75,0 +"confidence_interval_low",0.118117248757025,0.0125791170934251,0.194120449683243,0 +"confidence_interval_high",0.881882751242975,0.987420882906575,0.99369053679029,0.841886116991581
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/L.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,2,3,3 +"Lower",3,3,2,2 +"Difference",-1,-1,1,1 +"Trial_Number",5,5,5,5 +"p-value",1,1,1,1 +"probability_of_success",0.4,0.4,0.6,0.6 +"confidence_interval_low",0.0527449505263169,0.0527449505263169,0.146632799634673,0.146632799634673 +"confidence_interval_high",0.853367200365327,0.853367200365327,0.947255049473683,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/M.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,2,2,2 +"Lower",2,0,1,0 +"Difference",-1,2,1,2 +"Trial_Number",3,2,3,2 +"p-value",1,0.5,1,0.5 +"probability_of_success",0.333333333333333,1,0.666666666666667,1 +"confidence_interval_low",0.00840375865961264,0.158113883008419,0.0942993240502461,0.158113883008419 +"confidence_interval_high",0.905700675949754,1,0.991596241340387,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/N.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,4,2 +"Lower",2,0,2,0 +"Difference",-1,1,2,2 +"Trial_Number",3,1,6,2 +"p-value",1,1,0.6875,0.5 +"probability_of_success",0.333333333333333,1,0.666666666666667,1 +"confidence_interval_low",0.00840375865961264,0.025,0.222778095503512,0.158113883008419 +"confidence_interval_high",0.905700675949754,1,0.956728131707258,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/P.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,1,1 +"Lower",0,2,1,1 +"Difference",1,-1,0,0 +"Trial_Number",1,3,2,2 +"p-value",1,1,1,1 +"probability_of_success",1,0.333333333333333,0.5,0.5 +"confidence_interval_low",0.025,0.00840375865961264,0.0125791170934251,0.0125791170934251 +"confidence_interval_high",1,0.905700675949754,0.987420882906575,0.987420882906575
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/Q.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,3,3 +"Lower",1,3,1,4 +"Difference",0,-2,2,-1 +"Trial_Number",2,4,4,7 +"p-value",1,0.625,0.625,1 +"probability_of_success",0.5,0.25,0.75,0.428571428571429 +"confidence_interval_low",0.0125791170934251,0.00630946320970987,0.194120449683243,0.0989882784425079 +"confidence_interval_high",0.987420882906575,0.805879550316757,0.99369053679029,0.815948432359917
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/R.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,4,2,3 +"Lower",4,2,4,1 +"Difference",0,2,-2,2 +"Trial_Number",8,6,6,4 +"p-value",1,0.6875,0.6875,0.625 +"probability_of_success",0.5,0.666666666666667,0.333333333333333,0.75 +"confidence_interval_low",0.157012770487058,0.222778095503512,0.0432718682927417,0.194120449683243 +"confidence_interval_high",0.842987229512942,0.956728131707258,0.777221904496488,0.99369053679029
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/S.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,5,4,1 +"Lower",3,2,3,3 +"Difference",-1,3,1,-2 +"Trial_Number",5,7,7,4 +"p-value",1,0.453125,1,0.625 +"probability_of_success",0.4,0.714285714285714,0.571428571428571,0.25 +"confidence_interval_low",0.0527449505263169,0.290420863737343,0.184051567640083,0.00630946320970987 +"confidence_interval_high",0.853367200365327,0.963307433823914,0.901011721557492,0.805879550316757
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/T.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,4,2,2 +"Lower",2,2,2,3 +"Difference",0,2,0,-1 +"Trial_Number",4,6,4,5 +"p-value",1,0.6875,1,1 +"probability_of_success",0.5,0.666666666666667,0.5,0.4 +"confidence_interval_low",0.067585986488543,0.222778095503512,0.067585986488543,0.0527449505263169 +"confidence_interval_high",0.932414013511457,0.956728131707258,0.932414013511457,0.853367200365327
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/V.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,4,4,3 +"Lower",2,4,4,2 +"Difference",0,0,0,1 +"Trial_Number",4,8,8,5 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.5,0.5,0.6 +"confidence_interval_low",0.067585986488543,0.157012770487058,0.157012770487058,0.146632799634673 +"confidence_interval_high",0.932414013511457,0.842987229512942,0.842987229512942,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/W.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",0,0,0,0 +"Lower",0,1,0,0 +"Difference",0,-1,0,0 +"Trial_Number",0,1,0,0 +"p-value",NA,1,NA,NA +"probability_of_success",NA,0,NA,NA +"confidence_interval_low",NA,0,NA,NA +"confidence_interval_high",NA,0.975,NA,NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/Y.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,3,2,1 +"Lower",1,2,3,1 +"Difference",0,1,-1,0 +"Trial_Number",2,5,5,2 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.6,0.4,0.5 +"confidence_interval_low",0.0125791170934251,0.146632799634673,0.0527449505263169,0.0125791170934251 +"confidence_interval_high",0.987420882906575,0.947255049473683,0.853367200365327,0.987420882906575
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/AC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,1,3,5 +"Lower",1,4,5,0 +"Difference",4,-3,-2,5 +"Trial_Number",6,5,8,5 +"p-value",0.21875,0.375,0.7265625,0.0625 +"probability_of_success",0.833333333333333,0.2,0.375,1 +"confidence_interval_low",0.358765421002325,0.00505076337946806,0.0852334141372536,0.478176249895019 +"confidence_interval_high",0.995789255485511,0.716417936118089,0.755136783633448,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/APGC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,2,4,4 +"Lower",1,4,7,2 +"Difference",3,-2,-3,2 +"Trial_Number",5,6,11,6 +"p-value",0.375,0.6875,0.548828125,0.6875 +"probability_of_success",0.8,0.333333333333333,0.363636363636364,0.666666666666667 +"confidence_interval_low",0.283582063881911,0.0432718682927417,0.109263443819098,0.222778095503512 +"confidence_interval_high",0.994949236620532,0.777221904496488,0.692095284988323,0.956728131707258
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/AVLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,2,4,2 +"Lower",3,6,2,1 +"Difference",0,-4,2,1 +"Trial_Number",6,8,6,3 +"p-value",1,0.2890625,0.6875,1 +"probability_of_success",0.5,0.25,0.666666666666667,0.666666666666667 +"confidence_interval_low",0.118117248757025,0.0318540262499442,0.222778095503512,0.0942993240502461 +"confidence_interval_high",0.881882751242975,0.650855794412824,0.956728131707258,0.991596241340387
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,1,3,3 +"Lower",3,5,3,1 +"Difference",-1,-4,0,2 +"Trial_Number",5,6,6,4 +"p-value",1,0.21875,1,0.625 +"probability_of_success",0.4,0.166666666666667,0.5,0.75 +"confidence_interval_low",0.0527449505263169,0.00421074451448947,0.118117248757025,0.194120449683243 +"confidence_interval_high",0.853367200365327,0.641234578997675,0.881882751242975,0.99369053679029
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/DE.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,1,2,3 +"Lower",0,2,2,1 +"Difference",2,-1,0,2 +"Trial_Number",2,3,4,4 +"p-value",0.5,1,1,0.625 +"probability_of_success",1,0.333333333333333,0.5,0.75 +"confidence_interval_low",0.158113883008419,0.00840375865961264,0.067585986488543,0.194120449683243 +"confidence_interval_high",1,0.905700675949754,0.932414013511457,0.99369053679029
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/DNQTSHA.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,2,6,0 +"Lower",2,2,3,3 +"Difference",-1,0,3,-3 +"Trial_Number",3,4,9,3 +"p-value",1,1,0.5078125,0.25 +"probability_of_success",0.333333333333333,0.5,0.666666666666667,0 +"confidence_interval_low",0.00840375865961264,0.067585986488543,0.29929505620854,0 +"confidence_interval_high",0.905700675949754,0.932414013511457,0.925145368580308,0.707598226178713
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/EK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,2,2,2 +"Lower",2,2,3,3 +"Difference",1,0,-1,-1 +"Trial_Number",5,4,5,5 +"p-value",1,1,1,1 +"probability_of_success",0.6,0.5,0.4,0.4 +"confidence_interval_low",0.146632799634673,0.067585986488543,0.0527449505263169,0.0527449505263169 +"confidence_interval_high",0.947255049473683,0.932414013511457,0.853367200365327,0.853367200365327
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ERK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,3,3,2 +"Lower",3,2,4,5 +"Difference",1,1,-1,-3 +"Trial_Number",7,5,7,7 +"p-value",1,1,1,0.453125 +"probability_of_success",0.571428571428571,0.6,0.428571428571429,0.285714285714286 +"confidence_interval_low",0.184051567640083,0.146632799634673,0.0989882784425079,0.0366925661760856 +"confidence_interval_high",0.901011721557492,0.947255049473683,0.815948432359917,0.709579136262657
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/FYMINK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,2,5,5 +"Lower",5,2,1,2 +"Difference",-2,0,4,3 +"Trial_Number",8,4,6,7 +"p-value",0.7265625,1,0.21875,0.453125 +"probability_of_success",0.375,0.5,0.833333333333333,0.714285714285714 +"confidence_interval_low",0.0852334141372536,0.067585986488543,0.358765421002325,0.290420863737343 +"confidence_interval_high",0.755136783633448,0.932414013511457,0.995789255485511,0.963307433823914
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/FYW.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,2,1,2 +"Lower",2,3,2,1 +"Difference",0,-1,-1,1 +"Trial_Number",4,5,3,3 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.4,0.333333333333333,0.666666666666667 +"confidence_interval_low",0.067585986488543,0.0527449505263169,0.00840375865961264,0.0942993240502461 +"confidence_interval_high",0.932414013511457,0.853367200365327,0.905700675949754,0.991596241340387
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/GARP.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,4,2,6 +"Lower",3,7,4,1 +"Difference",1,-3,-2,5 +"Trial_Number",7,11,6,7 +"p-value",1,0.548828125,0.6875,0.125 +"probability_of_success",0.571428571428571,0.363636363636364,0.333333333333333,0.857142857142857 +"confidence_interval_low",0.184051567640083,0.109263443819098,0.0432718682927417,0.421276802956805 +"confidence_interval_high",0.901011721557492,0.692095284988323,0.777221904496488,0.996389703138099
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/IVYWREL.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,5,1,3 +"Lower",1,4,9,2 +"Difference",4,1,-8,1 +"Trial_Number",6,9,10,5 +"p-value",0.21875,1,0.021484375,1 +"probability_of_success",0.833333333333333,0.555555555555556,0.1,0.6 +"confidence_interval_low",0.358765421002325,0.212008506778868,0.00252857854446179,0.146632799634673 +"confidence_interval_high",0.995789255485511,0.863004337734833,0.445016117028195,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/QH.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,3,2,4 +"Lower",1,1,2,4 +"Difference",2,2,0,0 +"Trial_Number",4,4,4,8 +"p-value",0.625,0.625,1,1 +"probability_of_success",0.75,0.75,0.5,0.5 +"confidence_interval_low",0.194120449683243,0.194120449683243,0.067585986488543,0.157012770487058 +"confidence_interval_high",0.99369053679029,0.99369053679029,0.932414013511457,0.842987229512942
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/RHK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,4,0,3 +"Lower",2,1,4,2 +"Difference",1,3,-4,1 +"Trial_Number",5,5,4,5 +"p-value",1,0.375,0.125,1 +"probability_of_success",0.6,0.8,0,0.6 +"confidence_interval_low",0.146632799634673,0.283582063881911,0,0.146632799634673 +"confidence_interval_high",0.947255049473683,0.994949236620532,0.602364635616475,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/RHKDE.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,5,1,4 +"Lower",1,1,2,2 +"Difference",2,4,-1,2 +"Trial_Number",4,6,3,6 +"p-value",0.625,0.21875,1,0.6875 +"probability_of_success",0.75,0.833333333333333,0.333333333333333,0.666666666666667 +"confidence_interval_low",0.194120449683243,0.358765421002325,0.00840375865961264,0.222778095503512 +"confidence_interval_high",0.99369053679029,0.995789255485511,0.905700675949754,0.956728131707258
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/STNQ.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,4,4,3 +"Lower",4,2,3,8 +"Difference",-2,2,1,-5 +"Trial_Number",6,6,7,11 +"p-value",0.6875,0.6875,1,0.2265625 +"probability_of_success",0.333333333333333,0.666666666666667,0.571428571428571,0.272727272727273 +"confidence_interval_low",0.0432718682927417,0.222778095503512,0.184051567640083,0.0602177341729066 +"confidence_interval_high",0.777221904496488,0.956728131707258,0.901011721557492,0.609742559572421
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/VLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,5,4,2 +"Lower",2,3,3,2 +"Difference",1,2,1,0 +"Trial_Number",5,8,7,4 +"p-value",1,0.7265625,1,1 +"probability_of_success",0.6,0.625,0.571428571428571,0.5 +"confidence_interval_low",0.146632799634673,0.244863216366552,0.184051567640083,0.067585986488543 +"confidence_interval_high",0.947255049473683,0.914766585862746,0.901011721557492,0.932414013511457
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,3,5,8 +"Lower",4,9,9,1 +"Difference",2,-6,-4,7 +"Trial_Number",10,12,14,9 +"p-value",0.75390625,0.14599609375,0.4239501953125,0.0390625 +"probability_of_success",0.6,0.25,0.357142857142857,0.888888888888889 +"confidence_interval_low",0.262378076606945,0.0548606445279928,0.127598429859159,0.517503485082663 +"confidence_interval_high",0.878447741880173,0.571858461878189,0.648619889384008,0.997190863253401
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,2,5,8 +"Lower",5,7,9,2 +"Difference",0,-5,-4,6 +"Trial_Number",10,9,14,10 +"p-value",1,0.1796875,0.4239501953125,0.109375 +"probability_of_success",0.5,0.222222222222222,0.357142857142857,0.8 +"confidence_interval_low",0.187086028447399,0.0281449734778982,0.127598429859159,0.443904537692359 +"confidence_interval_high",0.812913971552601,0.600093573716312,0.648619889384008,0.974789273673167
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,3,2,5 +"Lower",4,3,4,4 +"Difference",-1,0,-2,1 +"Trial_Number",7,6,6,9 +"p-value",1,1,0.6875,1 +"probability_of_success",0.428571428571429,0.5,0.333333333333333,0.555555555555556 +"confidence_interval_low",0.0989882784425079,0.118117248757025,0.0432718682927417,0.212008506778868 +"confidence_interval_high",0.815948432359917,0.881882751242975,0.777221904496488,0.863004337734833
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,2,3,4 +"Lower",2,4,6,6 +"Difference",4,-2,-3,-2 +"Trial_Number",8,6,9,10 +"p-value",0.2890625,0.6875,0.5078125,0.75390625 +"probability_of_success",0.75,0.333333333333333,0.333333333333333,0.4 +"confidence_interval_low",0.349144205587176,0.0432718682927417,0.0748546314196918,0.121552258119827 +"confidence_interval_high",0.968145973750056,0.777221904496488,0.70070494379146,0.737621923393055
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,3,4,4 +"Lower",5,4,5,5 +"Difference",0,-1,-1,-1 +"Trial_Number",10,7,9,9 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.428571428571429,0.444444444444444,0.444444444444444 +"confidence_interval_low",0.187086028447399,0.0989882784425079,0.136995662265167,0.136995662265167 +"confidence_interval_high",0.812913971552601,0.815948432359917,0.787991493221132,0.787991493221132
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_hydratation.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,6,4,5 +"Lower",3,5,7,6 +"Difference",2,1,-3,-1 +"Trial_Number",8,11,11,11 +"p-value",0.7265625,1,0.548828125,1 +"probability_of_success",0.625,0.545454545454545,0.363636363636364,0.454545454545455 +"confidence_interval_low",0.244863216366552,0.233793597659345,0.109263443819098,0.167488094063707 +"confidence_interval_high",0.914766585862746,0.832511905936293,0.692095284988323,0.766206402340655
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,3,8,5 +"Lower",5,7,8,3 +"Difference",1,-4,0,2 +"Trial_Number",11,10,16,8 +"p-value",1,0.34375,1,0.7265625 +"probability_of_success",0.545454545454545,0.3,0.5,0.625 +"confidence_interval_low",0.233793597659345,0.0667395111777345,0.246510111490575,0.244863216366552 +"confidence_interval_high",0.832511905936293,0.652452850059997,0.753489888509425,0.914766585862746
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_residue_volume.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",7,6,5,5 +"Lower",4,6,11,3 +"Difference",3,0,-6,2 +"Trial_Number",11,12,16,8 +"p-value",0.548828125,1,0.210113525390625,0.7265625 +"probability_of_success",0.636363636363636,0.5,0.3125,0.625 +"confidence_interval_low",0.307904715011677,0.210944638239297,0.110169954717117,0.244863216366552 +"confidence_interval_high",0.890736556180902,0.789055361760703,0.586620636451359,0.914766585862746
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_residue_weight.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,6,5,6 +"Lower",5,6,8,5 +"Difference",1,0,-3,1 +"Trial_Number",11,12,13,11 +"p-value",1,1,0.5810546875,1 +"probability_of_success",0.545454545454545,0.5,0.384615384615385,0.545454545454545 +"confidence_interval_low",0.233793597659345,0.210944638239297,0.138579338890161,0.233793597659345 +"confidence_interval_high",0.832511905936293,0.789055361760703,0.684222397085937,0.832511905936293
--- a/test-data/OUT_aa/AVLIMFYW.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_AVLIMFYW,Ac_prop_AVLIMFYW,Ac_count_AVLIM,Ac_prop_AVLIM,Ac_count_FYW,Ac_prop_FYW,Pu_count_AVLIMFYW,Pu_prop_AVLIMFYW,Pu_count_AVLIM,Pu_prop_AVLIM,Pu_count_FYW,Pu_prop_FYW,Am_count_AVLIMFYW,Am_prop_AVLIMFYW,Am_count_AVLIM,Am_prop_AVLIM,Am_count_FYW,Am_prop_FYW,Ap_count_AVLIMFYW,Ap_prop_AVLIMFYW,Ap_count_AVLIM,Ap_prop_AVLIM,Ap_count_FYW,Ap_prop_FYW,Pf_count_AVLIMFYW,Pf_prop_AVLIMFYW,Pf_count_AVLIM,Pf_prop_AVLIM,Pf_count_FYW,Pf_prop_FYW,Pg_count_AVLIMFYW,Pg_prop_AVLIMFYW,Pg_count_AVLIM,Pg_prop_AVLIM,Pg_count_FYW,Pg_prop_FYW,Ph_count_AVLIMFYW,Ph_prop_AVLIMFYW,Ph_count_AVLIM,Ph_prop_AVLIM,Ph_count_FYW,Ph_prop_FYW,Ps_count_AVLIMFYW,Ps_prop_AVLIMFYW,Ps_count_AVLIM,Ps_prop_AVLIM,Ps_count_FYW,Ps_prop_FYW,Pp_count_AVLIMFYW,Pp_prop_AVLIMFYW,Pp_count_AVLIM,Pp_prop_AVLIM,Pp_count_FYW,Pp_prop_FYW,Pa_count_AVLIMFYW,Pa_prop_AVLIMFYW,Pa_count_AVLIM,Pa_prop_AVLIM,Pa_count_FYW,Pa_prop_FYW -locus2_sp6_sp6.fasta,27.00000,0.42188,21.00000,0.32812,6.00000,0.09375,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375 -locus1_sp6_sp6.fasta,25.00000,0.32051,22.00000,0.28205,3.00000,0.03846,25.00000,0.32051,23.00000,0.29487,2.00000,0.02564,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,25.00000,0.32051,23.00000,0.29487,2.00000,0.02564,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564 -locus1_sp8_sp8.fasta,23.00000,0.33824,21.00000,0.30882,2.00000,0.02941,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,29.00000,0.37662,26.00000,0.33766,3.00000,0.03896,30.00000,0.38961,27.00000,0.35065,3.00000,0.03896,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,24.00000,0.36364,22.00000,0.33333,2.00000,0.03030,29.00000,0.37662,26.00000,0.33766,3.00000,0.03896
--- a/test-data/OUT_aa/EK_QH.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_EK,Ac_prop_EK,Ac_count_QH,Ac_prop_QH,Ac_ratio_EK_vs_QH,Pu_count_EK,Pu_prop_EK,Pu_count_QH,Pu_prop_QH,Pu_ratio_EK_vs_QH,Am_count_EK,Am_prop_EK,Am_count_QH,Am_prop_QH,Am_ratio_EK_vs_QH,Ap_count_EK,Ap_prop_EK,Ap_count_QH,Ap_prop_QH,Ap_ratio_EK_vs_QH,Pf_count_EK,Pf_prop_EK,Pf_count_QH,Pf_prop_QH,Pf_ratio_EK_vs_QH,Pg_count_EK,Pg_prop_EK,Pg_count_QH,Pg_prop_QH,Pg_ratio_EK_vs_QH,Ph_count_EK,Ph_prop_EK,Ph_count_QH,Ph_prop_QH,Ph_ratio_EK_vs_QH,Ps_count_EK,Ps_prop_EK,Ps_count_QH,Ps_prop_QH,Ps_ratio_EK_vs_QH,Pp_count_EK,Pp_prop_EK,Pp_count_QH,Pp_prop_QH,Pp_ratio_EK_vs_QH,Pa_count_EK,Pa_prop_EK,Pa_count_QH,Pa_prop_QH,Pa_ratio_EK_vs_QH -locus2_sp6_sp6.fasta,13.00000,0.20312,2.00000,0.03125,6.50000,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,14.00000,0.21875,2.00000,0.03125,7.00000,13.00000,0.20312,2.00000,0.03125,6.50000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,14.00000,0.21875,2.00000,0.03125,7.00000 -locus1_sp6_sp6.fasta,10.00000,0.12821,11.00000,0.14103,0.90909,11.00000,0.14103,11.00000,0.14103,1.00000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,10.00000,0.12821,11.00000,0.14103,0.90909,10.00000,0.12821,11.00000,0.14103,0.90909,10.00000,0.12821,11.00000,0.14103,0.90909,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,10.00000,0.12821,11.00000,0.14103,0.90909 -locus1_sp8_sp8.fasta,8.00000,0.11765,4.00000,0.05882,2.00000,10.00000,0.12987,5.00000,0.06494,2.00000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,9.00000,0.11688,4.00000,0.05195,2.25000,9.00000,0.11688,5.00000,0.06494,1.80000,10.00000,0.12987,4.00000,0.05195,2.50000,0.00000,0.00000,0.00000,0.00000,0.00000,9.00000,0.13636,4.00000,0.06061,2.25000,9.00000,0.11688,5.00000,0.06494,1.80000
--- a/test-data/OUT_aa/ERK_DNQTSH.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_ERK,Ac_prop_ERK,Ac_count_DNQTSH,Ac_prop_DNQTSH,Ac_ratio_ERK_vs_DNQTSH,Pu_count_ERK,Pu_prop_ERK,Pu_count_DNQTSH,Pu_prop_DNQTSH,Pu_ratio_ERK_vs_DNQTSH,Am_count_ERK,Am_prop_ERK,Am_count_DNQTSH,Am_prop_DNQTSH,Am_ratio_ERK_vs_DNQTSH,Ap_count_ERK,Ap_prop_ERK,Ap_count_DNQTSH,Ap_prop_DNQTSH,Ap_ratio_ERK_vs_DNQTSH,Pf_count_ERK,Pf_prop_ERK,Pf_count_DNQTSH,Pf_prop_DNQTSH,Pf_ratio_ERK_vs_DNQTSH,Pg_count_ERK,Pg_prop_ERK,Pg_count_DNQTSH,Pg_prop_DNQTSH,Pg_ratio_ERK_vs_DNQTSH,Ph_count_ERK,Ph_prop_ERK,Ph_count_DNQTSH,Ph_prop_DNQTSH,Ph_ratio_ERK_vs_DNQTSH,Ps_count_ERK,Ps_prop_ERK,Ps_count_DNQTSH,Ps_prop_DNQTSH,Ps_ratio_ERK_vs_DNQTSH,Pp_count_ERK,Pp_prop_ERK,Pp_count_DNQTSH,Pp_prop_DNQTSH,Pp_ratio_ERK_vs_DNQTSH,Pa_count_ERK,Pa_prop_ERK,Pa_count_DNQTSH,Pa_prop_DNQTSH,Pa_ratio_ERK_vs_DNQTSH -locus2_sp6_sp6.fasta,13.00000,0.20312,14.00000,0.21875,0.92857,13.00000,0.20312,14.00000,0.21875,0.92857,NA,NA,NA,NA,NA,13.00000,0.20312,13.00000,0.20312,1.00000,NA,NA,NA,NA,NA,14.00000,0.21875,13.00000,0.20312,1.07692,13.00000,0.20312,14.00000,0.21875,0.92857,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,14.00000,0.21875,13.00000,0.20312,1.07692 -locus1_sp6_sp6.fasta,16.00000,0.20513,31.00000,0.39744,0.51613,18.00000,0.23077,27.00000,0.34615,0.66667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.23077,30.00000,0.38462,0.60000,17.00000,0.21795,31.00000,0.39744,0.54839,17.00000,0.21795,31.00000,0.39744,0.54839,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.21795,31.00000,0.39744,0.54839 -locus1_sp8_sp8.fasta,11.00000,0.16176,24.00000,0.35294,0.45833,11.00000,0.14286,31.00000,0.40260,0.35484,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,11.00000,0.14286,32.00000,0.41558,0.34375,10.00000,0.12987,30.00000,0.38961,0.33333,11.00000,0.14286,30.00000,0.38961,0.36667,0.00000,0.00000,0.00000,0.00000,0.00000,10.00000,0.15152,27.00000,0.40909,0.37037,10.00000,0.12987,31.00000,0.40260,0.32258
--- a/test-data/OUT_aa/FYMINK_GARP.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_FYMINK,Ac_prop_FYMINK,Ac_count_GARP,Ac_prop_GARP,Pu_count_FYMINK,Pu_prop_FYMINK,Pu_count_GARP,Pu_prop_GARP,Am_count_FYMINK,Am_prop_FYMINK,Am_count_GARP,Am_prop_GARP,Ap_count_FYMINK,Ap_prop_FYMINK,Ap_count_GARP,Ap_prop_GARP,Pf_count_FYMINK,Pf_prop_FYMINK,Pf_count_GARP,Pf_prop_GARP,Pg_count_FYMINK,Pg_prop_FYMINK,Pg_count_GARP,Pg_prop_GARP,Ph_count_FYMINK,Ph_prop_FYMINK,Ph_count_GARP,Ph_prop_GARP,Ps_count_FYMINK,Ps_prop_FYMINK,Ps_count_GARP,Ps_prop_GARP,Pp_count_FYMINK,Pp_prop_FYMINK,Pp_count_GARP,Pp_prop_GARP,Pa_count_FYMINK,Pa_prop_FYMINK,Pa_count_GARP,Pa_prop_GARP -locus2_sp6_sp6.fasta,21.00000,0.32812,16.00000,0.25000,20.00000,0.31250,15.00000,0.23438,NA,NA,NA,NA,21.00000,0.32812,16.00000,0.25000,NA,NA,NA,NA,21.00000,0.32812,15.00000,0.23438,20.00000,0.31250,15.00000,0.23438,NA,NA,NA,NA,NA,NA,NA,NA,21.00000,0.32812,15.00000,0.23438 -locus1_sp6_sp6.fasta,15.00000,0.19231,17.00000,0.21795,12.00000,0.15385,20.00000,0.25641,NA,NA,NA,NA,NA,NA,NA,NA,13.00000,0.16667,19.00000,0.24359,13.00000,0.16667,18.00000,0.23077,12.00000,0.15385,18.00000,0.23077,NA,NA,NA,NA,NA,NA,NA,NA,13.00000,0.16667,18.00000,0.23077 -locus1_sp8_sp8.fasta,14.00000,0.20588,16.00000,0.23529,16.00000,0.20779,12.00000,0.15584,NA,NA,NA,NA,NA,NA,NA,NA,15.00000,0.19481,13.00000,0.16883,12.00000,0.15584,15.00000,0.19481,17.00000,0.22078,14.00000,0.18182,0.00000,0.00000,0.00000,0.00000,12.00000,0.18182,8.00000,0.12121,12.00000,0.15584,14.00000,0.18182
--- a/test-data/OUT_aa/IVYWREL.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_IVYWREL,Ac_prop_IVYWREL,Pu_count_IVYWREL,Pu_prop_IVYWREL,Am_count_IVYWREL,Am_prop_IVYWREL,Ap_count_IVYWREL,Ap_prop_IVYWREL,Pf_count_IVYWREL,Pf_prop_IVYWREL,Pg_count_IVYWREL,Pg_prop_IVYWREL,Ph_count_IVYWREL,Ph_prop_IVYWREL,Ps_count_IVYWREL,Ps_prop_IVYWREL,Pp_count_IVYWREL,Pp_prop_IVYWREL,Pa_count_IVYWREL,Pa_prop_IVYWREL -locus2_sp6_sp6.fasta,21.00000,0.32812,23.00000,0.35938,NA,NA,23.00000,0.35938,NA,NA,22.00000,0.34375,23.00000,0.35938,NA,NA,NA,NA,22.00000,0.34375 -locus1_sp6_sp6.fasta,29.00000,0.37179,31.00000,0.39744,NA,NA,NA,NA,29.00000,0.37179,28.00000,0.35897,29.00000,0.37179,NA,NA,NA,NA,28.00000,0.35897 -locus1_sp8_sp8.fasta,25.00000,0.36765,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065
--- a/test-data/OUT_aa/PAYRE-MVGDS.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_PAYRE,Ac_prop_PAYRE,Ac_count_AC,Ac_prop_AC,Ac_count_MVGDS,Ac_prop_MVGDS,Ac_ratio_PAYRE_vs_MVGDS,Ac_ratio_AC_vs_MVGDS,Pu_count_PAYRE,Pu_prop_PAYRE,Pu_count_AC,Pu_prop_AC,Pu_count_MVGDS,Pu_prop_MVGDS,Pu_ratio_PAYRE_vs_MVGDS,Pu_ratio_AC_vs_MVGDS,Am_count_PAYRE,Am_prop_PAYRE,Am_count_AC,Am_prop_AC,Am_count_MVGDS,Am_prop_MVGDS,Am_ratio_PAYRE_vs_MVGDS,Am_ratio_AC_vs_MVGDS,Ap_count_PAYRE,Ap_prop_PAYRE,Ap_count_AC,Ap_prop_AC,Ap_count_MVGDS,Ap_prop_MVGDS,Ap_ratio_PAYRE_vs_MVGDS,Ap_ratio_AC_vs_MVGDS,Pf_count_PAYRE,Pf_prop_PAYRE,Pf_count_AC,Pf_prop_AC,Pf_count_MVGDS,Pf_prop_MVGDS,Pf_ratio_PAYRE_vs_MVGDS,Pf_ratio_AC_vs_MVGDS,Pg_count_PAYRE,Pg_prop_PAYRE,Pg_count_AC,Pg_prop_AC,Pg_count_MVGDS,Pg_prop_MVGDS,Pg_ratio_PAYRE_vs_MVGDS,Pg_ratio_AC_vs_MVGDS,Ph_count_PAYRE,Ph_prop_PAYRE,Ph_count_AC,Ph_prop_AC,Ph_count_MVGDS,Ph_prop_MVGDS,Ph_ratio_PAYRE_vs_MVGDS,Ph_ratio_AC_vs_MVGDS,Ps_count_PAYRE,Ps_prop_PAYRE,Ps_count_AC,Ps_prop_AC,Ps_count_MVGDS,Ps_prop_MVGDS,Ps_ratio_PAYRE_vs_MVGDS,Ps_ratio_AC_vs_MVGDS,Pp_count_PAYRE,Pp_prop_PAYRE,Pp_count_AC,Pp_prop_AC,Pp_count_MVGDS,Pp_prop_MVGDS,Pp_ratio_PAYRE_vs_MVGDS,Pp_ratio_AC_vs_MVGDS,Pa_count_PAYRE,Pa_prop_PAYRE,Pa_count_AC,Pa_prop_AC,Pa_count_MVGDS,Pa_prop_MVGDS,Pa_ratio_PAYRE_vs_MVGDS,Pa_ratio_AC_vs_MVGDS -locus2_sp6_sp6.fasta,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,18.00000,0.28125,6.00000,0.09375,21.00000,0.32812,0.85714,0.28571,NA,NA,NA,NA,NA,NA,NA,NA,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000,20.00000,0.31250,8.00000,0.12500,19.00000,0.29688,1.05263,0.42105,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,17.00000,0.26562,6.00000,0.09375,20.00000,0.31250,0.85000,0.30000 -locus1_sp6_sp6.fasta,24.00000,0.30769,7.00000,0.08974,20.00000,0.25641,1.20000,0.35000,25.00000,0.32051,7.00000,0.08974,20.00000,0.25641,1.25000,0.35000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,25.00000,0.32051,8.00000,0.10256,21.00000,0.26923,1.19048,0.38095,24.00000,0.30769,7.00000,0.08974,22.00000,0.28205,1.09091,0.31818,24.00000,0.30769,7.00000,0.08974,20.00000,0.25641,1.20000,0.35000,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,24.00000,0.30769,7.00000,0.08974,22.00000,0.28205,1.09091,0.31818 -locus1_sp8_sp8.fasta,16.00000,0.23529,3.00000,0.04412,27.00000,0.39706,0.59259,0.11111,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,19.00000,0.24675,6.00000,0.07792,30.00000,0.38961,0.63333,0.20000,20.00000,0.25974,7.00000,0.09091,32.00000,0.41558,0.62500,0.21875,20.00000,0.25974,5.00000,0.06494,29.00000,0.37662,0.68966,0.17241,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.21212,2.00000,0.03030,26.00000,0.39394,0.53846,0.07692,19.00000,0.24675,6.00000,0.07792,32.00000,0.41558,0.59375,0.18750
--- a/test-data/OUT_aa/RHKDE.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_RHKDE,Ac_prop_RHKDE,Ac_count_RHK,Ac_prop_RHK,Ac_count_DE,Ac_prop_DE,Pu_count_RHKDE,Pu_prop_RHKDE,Pu_count_RHK,Pu_prop_RHK,Pu_count_DE,Pu_prop_DE,Am_count_RHKDE,Am_prop_RHKDE,Am_count_RHK,Am_prop_RHK,Am_count_DE,Am_prop_DE,Ap_count_RHKDE,Ap_prop_RHKDE,Ap_count_RHK,Ap_prop_RHK,Ap_count_DE,Ap_prop_DE,Pf_count_RHKDE,Pf_prop_RHKDE,Pf_count_RHK,Pf_prop_RHK,Pf_count_DE,Pf_prop_DE,Pg_count_RHKDE,Pg_prop_RHKDE,Pg_count_RHK,Pg_prop_RHK,Pg_count_DE,Pg_prop_DE,Ph_count_RHKDE,Ph_prop_RHKDE,Ph_count_RHK,Ph_prop_RHK,Ph_count_DE,Ph_prop_DE,Ps_count_RHKDE,Ps_prop_RHKDE,Ps_count_RHK,Ps_prop_RHK,Ps_count_DE,Ps_prop_DE,Pp_count_RHKDE,Pp_prop_RHKDE,Pp_count_RHK,Pp_prop_RHK,Pp_count_DE,Pp_prop_DE,Pa_count_RHKDE,Pa_prop_RHKDE,Pa_count_RHK,Pa_prop_RHK,Pa_count_DE,Pa_prop_DE -locus2_sp6_sp6.fasta,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625 -locus1_sp6_sp6.fasta,28.00000,0.35897,14.00000,0.17949,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949 -locus1_sp8_sp8.fasta,14.00000,0.20588,4.00000,0.05882,10.00000,0.14706,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,16.00000,0.20779,5.00000,0.06494,11.00000,0.14286,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286,14.00000,0.18182,2.00000,0.02597,12.00000,0.15584,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,13.00000,0.19697,2.00000,0.03030,11.00000,0.16667,15.00000,0.19481,4.00000,0.05195,11.00000,0.14286
--- a/test-data/OUT_aa/STNQ.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_count_STNQ,Ac_prop_STNQ,Pu_count_STNQ,Pu_prop_STNQ,Am_count_STNQ,Am_prop_STNQ,Ap_count_STNQ,Ap_prop_STNQ,Pf_count_STNQ,Pf_prop_STNQ,Pg_count_STNQ,Pg_prop_STNQ,Ph_count_STNQ,Ph_prop_STNQ,Ps_count_STNQ,Ps_prop_STNQ,Pp_count_STNQ,Pp_prop_STNQ,Pa_count_STNQ,Pa_prop_STNQ -locus2_sp6_sp6.fasta,8.00000,0.12500,8.00000,0.12500,NA,NA,7.00000,0.10938,NA,NA,7.00000,0.10938,8.00000,0.12500,NA,NA,NA,NA,7.00000,0.10938 -locus1_sp6_sp6.fasta,19.00000,0.24359,15.00000,0.19231,NA,NA,NA,NA,18.00000,0.23077,18.00000,0.23077,18.00000,0.23077,NA,NA,NA,NA,18.00000,0.23077 -locus1_sp8_sp8.fasta,21.00000,0.30882,28.00000,0.36364,NA,NA,NA,NA,27.00000,0.35065,25.00000,0.32468,27.00000,0.35065,0.00000,0.00000,24.00000,0.36364,26.00000,0.33766
--- a/test-data/OUT_aa/TotalHydratation.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_Total_Hydratation,Pu_Total_Hydratation,Am_Total_Hydratation,Ap_Total_Hydratation,Pf_Total_Hydratation,Pg_Total_Hydratation,Ph_Total_Hydratation,Ps_Total_Hydratation,Pp_Total_Hydratation,Pa_Total_Hydratation -locus2_sp6_sp6.fasta,171.50000,171.50000,NA,170.50000,NA,171.00000,171.50000,NA,NA,171.00000 -locus1_sp6_sp6.fasta,224.00000,224.50000,NA,NA,223.00000,226.00000,226.00000,NA,NA,226.00000 -locus1_sp8_sp8.fasta,163.00000,188.00000,NA,NA,190.50000,188.50000,192.00000,0.00000,167.50000,189.50000
--- a/test-data/OUT_aa/TotalPartialSpecificVolume.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_Total_Partial_Specific_Volume,Pu_Total_Partial_Specific_Volume,Am_Total_Partial_Specific_Volume,Ap_Total_Partial_Specific_Volume,Pf_Total_Partial_Specific_Volume,Pg_Total_Partial_Specific_Volume,Ph_Total_Partial_Specific_Volume,Ps_Total_Partial_Specific_Volume,Pp_Total_Partial_Specific_Volume,Pa_Total_Partial_Specific_Volume -locus2_sp6_sp6.fasta,47.40000,47.77000,NA,47.71000,NA,48.17000,47.97000,NA,NA,48.17000 -locus1_sp6_sp6.fasta,56.53000,56.56000,NA,NA,56.37000,56.43000,56.54000,NA,NA,56.43000 -locus1_sp8_sp8.fasta,49.95000,56.86000,NA,NA,56.93000,57.09000,56.25000,0.00000,49.09000,57.05000
--- a/test-data/OUT_aa/TotalResidueVolume.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_Total_Residue_Volume,Pu_Total_Residue_Volume,Am_Total_Residue_Volume,Ap_Total_Residue_Volume,Pf_Total_Residue_Volume,Pg_Total_Residue_Volume,Ph_Total_Residue_Volume,Ps_Total_Residue_Volume,Pp_Total_Residue_Volume,Pa_Total_Residue_Volume -locus2_sp6_sp6.fasta,6575.00000,6593.00000,NA,6587.00000,NA,6645.00000,6631.00000,NA,NA,6645.00000 -locus1_sp6_sp6.fasta,8265.00000,8257.00000,NA,NA,8305.00000,8257.00000,8277.00000,NA,NA,8257.00000 -locus1_sp8_sp8.fasta,6699.00000,7671.00000,NA,NA,7642.00000,7493.00000,7561.00000,0.00000,6633.00000,7519.00000
--- a/test-data/OUT_aa/TotalResidueWeight.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_Total_Residue_Weight,Pu_Total_Residue_Weight,Am_Total_Residue_Weight,Ap_Total_Residue_Weight,Pf_Total_Residue_Weight,Pg_Total_Residue_Weight,Ph_Total_Residue_Weight,Ps_Total_Residue_Weight,Pp_Total_Residue_Weight,Pa_Total_Residue_Weight -locus2_sp6_sp6.fasta,6981.51000,6977.50000,NA,6961.51000,NA,6990.69000,7005.54000,NA,NA,6990.69000 -locus1_sp6_sp6.fasta,8981.54000,8937.66000,NA,NA,9023.69000,8989.64000,8985.64000,NA,NA,8989.64000 -locus1_sp8_sp8.fasta,7216.76000,8270.91000,NA,NA,8248.86000,8082.66000,8213.63000,0.00000,7124.55000,8112.69000
--- a/test-data/OUT_aa/prot_compositions_All_AA.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_prop_K,Ac_prop_R,Ac_prop_A,Ac_prop_F,Ac_prop_I,Ac_prop_L,Ac_prop_M,Ac_prop_V,Ac_prop_W,Ac_prop_N,Ac_prop_Q,Ac_prop_S,Ac_prop_T,Ac_prop_H,Ac_prop_Y,Ac_prop_C,Ac_prop_D,Ac_prop_E,Ac_prop_P,Ac_prop_G,Pu_prop_K,Pu_prop_R,Pu_prop_A,Pu_prop_F,Pu_prop_I,Pu_prop_L,Pu_prop_M,Pu_prop_V,Pu_prop_W,Pu_prop_N,Pu_prop_Q,Pu_prop_S,Pu_prop_T,Pu_prop_H,Pu_prop_Y,Pu_prop_C,Pu_prop_D,Pu_prop_E,Pu_prop_P,Pu_prop_G,Am_prop_K,Am_prop_R,Am_prop_A,Am_prop_F,Am_prop_I,Am_prop_L,Am_prop_M,Am_prop_V,Am_prop_W,Am_prop_N,Am_prop_Q,Am_prop_S,Am_prop_T,Am_prop_H,Am_prop_Y,Am_prop_C,Am_prop_D,Am_prop_E,Am_prop_P,Am_prop_G,Ap_prop_K,Ap_prop_R,Ap_prop_A,Ap_prop_F,Ap_prop_I,Ap_prop_L,Ap_prop_M,Ap_prop_V,Ap_prop_W,Ap_prop_N,Ap_prop_Q,Ap_prop_S,Ap_prop_T,Ap_prop_H,Ap_prop_Y,Ap_prop_C,Ap_prop_D,Ap_prop_E,Ap_prop_P,Ap_prop_G,Pf_prop_K,Pf_prop_R,Pf_prop_A,Pf_prop_F,Pf_prop_I,Pf_prop_L,Pf_prop_M,Pf_prop_V,Pf_prop_W,Pf_prop_N,Pf_prop_Q,Pf_prop_S,Pf_prop_T,Pf_prop_H,Pf_prop_Y,Pf_prop_C,Pf_prop_D,Pf_prop_E,Pf_prop_P,Pf_prop_G,Pg_prop_K,Pg_prop_R,Pg_prop_A,Pg_prop_F,Pg_prop_I,Pg_prop_L,Pg_prop_M,Pg_prop_V,Pg_prop_W,Pg_prop_N,Pg_prop_Q,Pg_prop_S,Pg_prop_T,Pg_prop_H,Pg_prop_Y,Pg_prop_C,Pg_prop_D,Pg_prop_E,Pg_prop_P,Pg_prop_G,Ph_prop_K,Ph_prop_R,Ph_prop_A,Ph_prop_F,Ph_prop_I,Ph_prop_L,Ph_prop_M,Ph_prop_V,Ph_prop_W,Ph_prop_N,Ph_prop_Q,Ph_prop_S,Ph_prop_T,Ph_prop_H,Ph_prop_Y,Ph_prop_C,Ph_prop_D,Ph_prop_E,Ph_prop_P,Ph_prop_G,Ps_prop_K,Ps_prop_R,Ps_prop_A,Ps_prop_F,Ps_prop_I,Ps_prop_L,Ps_prop_M,Ps_prop_V,Ps_prop_W,Ps_prop_N,Ps_prop_Q,Ps_prop_S,Ps_prop_T,Ps_prop_H,Ps_prop_Y,Ps_prop_C,Ps_prop_D,Ps_prop_E,Ps_prop_P,Ps_prop_G,Pp_prop_K,Pp_prop_R,Pp_prop_A,Pp_prop_F,Pp_prop_I,Pp_prop_L,Pp_prop_M,Pp_prop_V,Pp_prop_W,Pp_prop_N,Pp_prop_Q,Pp_prop_S,Pp_prop_T,Pp_prop_H,Pp_prop_Y,Pp_prop_C,Pp_prop_D,Pp_prop_E,Pp_prop_P,Pp_prop_G,Pa_prop_K,Pa_prop_R,Pa_prop_A,Pa_prop_F,Pa_prop_I,Pa_prop_L,Pa_prop_M,Pa_prop_V,Pa_prop_W,Pa_prop_N,Pa_prop_Q,Pa_prop_S,Pa_prop_T,Pa_prop_H,Pa_prop_Y,Pa_prop_C,Pa_prop_D,Pa_prop_E,Pa_prop_P,Pa_prop_G -locus2_sp6_sp6.fasta,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.03125,0.07812,0.00000,0.04688,0.01562,0.03125,0.03125,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,0.12500,0.00000,0.09375,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.07812,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.12500,0.00000,0.09375,0.04688,0.04688,0.09375,0.01562,0.09375,0.00000,0.04688,0.01562,0.03125,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.09375,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812,0.12500,0.00000,0.12500,0.04688,0.03125,0.09375,0.01562,0.10938,0.00000,0.04688,0.01562,0.04688,0.01562,0.01562,0.04688,0.00000,0.07812,0.07812,0.06250,0.04688,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.14062,0.00000,0.09375,0.06250,0.04688,0.09375,0.01562,0.09375,0.00000,0.03125,0.01562,0.04688,0.01562,0.01562,0.03125,0.00000,0.07812,0.07812,0.06250,0.07812 -locus1_sp6_sp6.fasta,0.03846,0.07692,0.07692,0.01282,0.03846,0.11538,0.02564,0.02564,0.00000,0.05128,0.07692,0.08974,0.02564,0.06410,0.02564,0.01282,0.08974,0.08974,0.03846,0.02564,0.03846,0.08974,0.07692,0.01282,0.01282,0.12821,0.02564,0.05128,0.00000,0.05128,0.06410,0.05128,0.02564,0.07692,0.01282,0.01282,0.07692,0.10256,0.03846,0.05128,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.03846,0.10256,0.08974,0.01282,0.01282,0.11538,0.03846,0.03846,0.00000,0.05128,0.07692,0.07692,0.02564,0.06410,0.01282,0.01282,0.08974,0.08974,0.02564,0.02564,0.03846,0.08974,0.07692,0.01282,0.01282,0.11538,0.03846,0.03846,0.00000,0.05128,0.06410,0.08974,0.02564,0.07692,0.01282,0.01282,0.08974,0.08974,0.03846,0.02564,0.03846,0.08974,0.07692,0.01282,0.01282,0.12821,0.02564,0.03846,0.00000,0.05128,0.06410,0.07692,0.03846,0.07692,0.01282,0.01282,0.08974,0.08974,0.03846,0.02564,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.03846,0.08974,0.07692,0.01282,0.01282,0.11538,0.03846,0.03846,0.00000,0.05128,0.06410,0.08974,0.02564,0.07692,0.01282,0.01282,0.08974,0.08974,0.03846,0.02564 -locus1_sp8_sp8.fasta,0.01471,0.04412,0.04412,0.02941,0.05882,0.07353,0.04412,0.08824,0.00000,0.05882,0.05882,0.11765,0.07353,0.00000,0.00000,0.00000,0.04412,0.10294,0.04412,0.10294,0.02597,0.01299,0.05195,0.01299,0.02597,0.10390,0.05195,0.09091,0.00000,0.06494,0.05195,0.15584,0.09091,0.01299,0.02597,0.00000,0.02597,0.10390,0.03896,0.05195,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,0.02597,0.02597,0.07792,0.01299,0.03896,0.10390,0.05195,0.06494,0.00000,0.03896,0.03896,0.18182,0.09091,0.01299,0.02597,0.00000,0.05195,0.09091,0.02597,0.03896,0.02597,0.01299,0.09091,0.01299,0.02597,0.10390,0.03896,0.09091,0.00000,0.02597,0.05195,0.18182,0.06494,0.01299,0.02597,0.00000,0.05195,0.09091,0.03896,0.05195,0.01299,0.01299,0.06494,0.01299,0.02597,0.10390,0.05195,0.07792,0.00000,0.09091,0.05195,0.14286,0.06494,0.00000,0.02597,0.00000,0.03896,0.11688,0.03896,0.06494,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.01515,0.01515,0.03030,0.01515,0.04545,0.12121,0.04545,0.09091,0.00000,0.04545,0.06061,0.16667,0.09091,0.00000,0.01515,0.00000,0.04545,0.12121,0.03030,0.04545,0.02597,0.01299,0.07792,0.01299,0.02597,0.10390,0.03896,0.09091,0.00000,0.02597,0.05195,0.18182,0.07792,0.01299,0.02597,0.00000,0.05195,0.09091,0.03896,0.05195
--- a/test-data/OUT_concat/.Rhistory Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,215 +0,0 @@ -shinyApp(ui=ui, server=server) -library(shiny) -library(shinythemes) -library(ggplot2) -library(FactoMineR) -library(factoextra) -library(shiny); runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -library(shiny); runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -2391+982+546+470+494+470+425+303+158+82+19 -494+470+425+303+158+82+19 -exclude <- c() # for X -> X -above <- c() # for X -> Y -below <- c() # for Y -> X -for (i in seq(1,400, by=21)) { -exclude <- c(exclude, i) -} -j <- 21 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- j*2+1 -print(paste(i, j, collapse=" ")) -} -j <- 21 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i*2+1 -print(paste(i, j, collapse=" ")) -} -j <- 21 -below <- c(21) # for Y -> X -for (i in seq(41,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i*2+1 -print(paste(i, j, collapse=" ")) -} -below <- c() # for Y -> X -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -} -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -below <- c(below, seq(i,j)) -} -below -length(below) -seq(101,105) -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -print(seq(i,j)) -below <- c(below, seq(i,j)) -} -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -print(seq(i,j)) -print lengt(seq(i,j)) -below <- c(below, seq(i,j)) -} -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -print(seq(i,j)) -print(length(seq(i,j))) -below <- c(below, seq(i,j)) -} -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -library(shiny); runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/shinyApp_Transitions.R') -substr('atgc', 0,2) -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/shinyApp_Transitions.R') -detach("package:shinyWidgets", unload=TRUE) -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/shinyApp_Transitions.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/shinyApp_Transitions.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -grep1('transitions', 'aatypes_transitions.csv') -grepl'transitions', 'aatypes_transitions.csv') -grepl('transitions', 'aatypes_transitions.csv') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -detach("package:shinyWidgets", unload=TRUE) -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/pca_plotly_Shiny.R') -library(shiny); runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/Results/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/Results/pca_plotly_Shiny.R') -runApp('Documents/Dev/script_alexis/corrected_files/corrected_files/Results/shinyApp_Transitions.R') -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -install.packages('httpuv') -install.packages("httpuv") -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -library("shinythemes", lib.loc="~/miniconda2/envs/env_R/lib/R/library") -library("plotly", lib.loc="~/miniconda2/envs/env_R/lib/R/library") -library("FactoMineR", lib.loc="~/miniconda2/envs/env_R/lib/R/library") -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -install.packages("FactoMineR") -install.packages('FactoMineR') -install.packages("~/Téléchargements/FactoMineR_1.40.tar.gz", repos = NULL, type = "source") -library("FactoMineR", lib.loc="~/miniconda2/envs/env_R2/lib/R/library") -install.packages("plotly") -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -install.packages("DT") -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -?scale -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny_v2.R') -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/Barplots_Transitions/scripts/barplots_plotly_Shiny.R') -setwd("~/Documents/Fork_AdaptSearch/adaptsearch/galaxy_wrappers/07_MutCount/test-data/sep_aa") -setwd("~/Documents/Fork_AdaptSearch/adaptsearch/galaxy_wrappers/07_MutCount/test-data/OUT_aa") -data <- read.table("prot_compositions_All_AA.csv", sep=",", header="T", dec=".") -data <- read.table("prot_compositions_All_AA.csv", sep=",", head="T", dec=".") -data <- read.table("prot_compositions_All_AA.csv", sep=",", header=T, dec=".") -View(data) -setwd("~/Documents") -data <- read.table("nuc_composition.csv", sep=",", header=T, dec=".") -data <- read.table("nuc_compositions.csv", sep=",", header=T, dec=".") -View(data) -data <- read.table('nuc_compositions.csv', sep=',', header=T, dec='.') -View(data) -res.pca <- PCA(data, scale.unit=TRUE, graph=T, axes=c(1,2)) -library(FactoMineR) -res.pca <- PCA(data, scale.unit=TRUE, graph=T, axes=c(1,2)) -runApp('Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -View(data) -data <- read.table("aa_freqs.csv", header=T, sep=',', dec='.') -setwd("~/Documents/Fork_AdaptSearch/adaptsearch/galaxy_wrappers/07_MutCount/test-data/OUT_concat") -data <- read.table("aa_freqs.csv", header=T, sep=',', dec='.') -repca <- PCA(data, scale.unit=TRUE, graph=T, axes=c(1,2)) -View(data) -data <- read.table("aa_freqs.csv", header=T, sep=',', dec='.', row.names=1) -repca <- PCA(data, scale.unit=TRUE, graph=T, axes=c(1,2)) -data_sel <- data[seq(2, nrow(data), 3),] -repca <- PCA(data, scale.unit=TRUE, graph=T, axes=c(1,2)) -repca <- PCA(data_sel, scale.unit=TRUE, graph=T, axes=c(1,2)) -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/PCA/scripts/pca_plotly_Shiny_v2.R') -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/Barplots_Transitions/scripts/barplots_plotly_Shiny.R') -runApp('~/Documents/Fork_AdaptSearch/adaptsearch/visualisation/Barplots_Transitions/scripts/barplots_plotly_Shiny.R')
--- a/test-data/OUT_nuc/.Rhistory Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ -shinyApp(ui=ui, server=server) -library(shiny) -library(shinythemes) -library(ggplot2) -library(FactoMineR) -library(factoextra) -library(shiny); runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -library(shiny); runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -runApp('Documents/Dev/adaptsearch_visualisation_existant/shinyApp/pcaShiny.R') -2391+982+546+470+494+470+425+303+158+82+19 -494+470+425+303+158+82+19 -exclude <- c() # for X -> X -above <- c() # for X -> Y -below <- c() # for Y -> X -for (i in seq(1,400, by=21)) { -exclude <- c(exclude, i) -} -j <- 21 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- j*2+1 -print(paste(i, j, collapse=" ")) -} -j <- 21 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i*2+1 -print(paste(i, j, collapse=" ")) -} -j <- 21 -below <- c(21) # for Y -> X -for (i in seq(41,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i*2+1 -print(paste(i, j, collapse=" ")) -} -below <- c() # for Y -> X -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -} -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -below <- c(below, seq(i,j)) -} -below -length(below) -seq(101,105) -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -print(seq(i,j)) -below <- c(below, seq(i,j)) -} -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -print(seq(i,j)) -print lengt(seq(i,j)) -below <- c(below, seq(i,j)) -} -j <- 21 -k <- 0 -for (i in seq(21,400, by=20)){ -below <- c(below, seq(i,j)) -j <- i+k -k <- k+1 -print(paste(i, j, collapse=" ")) -print(seq(i,j)) -print(length(seq(i,j))) -below <- c(below, seq(i,j)) -} -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -library(shiny); runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/barplots/barplots_plotly_Shiny.R') -runApp('Documents/Fork_AdaptSearch/adaptsearch/visualisation/pca/pca_plotly_Shiny.R') -to_plot <- melt(data, id_varaible="LOCUS") -library(ggplot2) -library(shiny) -library(reshape2) -library(rbokeh) -setwd("~/Documents/Fork_AdaptSearch/adaptsearch/galaxy_wrappers/07_MutCount/test-data/OUT_nuc") -data <- read.table("nuc_compositions.csv", header=T, sep=",", dec=".") -View(data) -?read.table -data <- read.table("nuc_compositions.csv", header=T, sep=",", dec=".", na.strings=c("NA")) -View(data) -to_plot <- melt(data, id_variable="LOCUS") -to_plot -data[,1] -data[,1]*4 -c(data[,1]) -c(data[,1], data[,1], data[,1]) -(data[,1], data[,1], data[,1]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,-3,NaN,-2,NaN +orthogroup_544_with_4_species.fasta,33,37,32,30 +orthogroup_546_with_4_species.fasta,-1,6,3,3 +orthogroup_761_with_4_species.fasta,16,13,21,31 +orthogroup_299_with_2_species.fasta,-2,-7,NaN,NaN +orthogroup_404_with_4_species.fasta,-16,-14,-15,-16 +orthogroup_316_with_4_species.fasta,90,92,91,87 +orthogroup_487_with_4_species.fasta,-2,-4,-2,3 +orthogroup_109_with_3_species.fasta,-3,7,NaN,-5 +orthogroup_696_with_4_species.fasta,12,9,20,7 +orthogroup_442_with_4_species.fasta,20,15,17,8 +orthogroup_508_with_4_species.fasta,-18,-13,-21,-14 +orthogroup_588_with_4_species.fasta,9,20,-15,6 +orthogroup_727_with_4_species.fasta,10,9,9,12 +orthogroup_335_with_4_species.fasta,-21,-10,-5,-4 +orthogroup_660_with_4_species.fasta,4,1,1,1 +orthogroup_623_with_4_species.fasta,1,6,-3,2 +orthogroup_283_with_2_species.fasta,NaN,-2,-7,NaN +orthogroup_651_with_4_species.fasta,0,4,4,2 +orthogroup_368_with_4_species.fasta,3,13,8,11 +orthogroup_343_with_4_species.fasta,0,3,1,-6 +orthogroup_301_with_4_species.fasta,14,13,9,6 +orthogroup_707_with_4_species.fasta,-7,1,-4,-2 +orthogroup_113_with_4_species.fasta,10,21,22,29
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,10,NaN,9,NaN +orthogroup_544_with_4_species.fasta,13,7,22,26 +orthogroup_546_with_4_species.fasta,-5,-4,-19,-11 +orthogroup_761_with_4_species.fasta,-3,-22,-8,-20 +orthogroup_299_with_2_species.fasta,-4,15,NaN,NaN +orthogroup_404_with_4_species.fasta,-2,-2,-7,0 +orthogroup_316_with_4_species.fasta,26,26,9,35 +orthogroup_487_with_4_species.fasta,3,5,7,2 +orthogroup_109_with_3_species.fasta,15,17,NaN,15 +orthogroup_696_with_4_species.fasta,-7,-8,-25,-18 +orthogroup_442_with_4_species.fasta,-8,-1,-13,-2 +orthogroup_508_with_4_species.fasta,-16,-15,-7,-10 +orthogroup_588_with_4_species.fasta,-50,-99,-102,-45 +orthogroup_727_with_4_species.fasta,-2,7,13,12 +orthogroup_335_with_4_species.fasta,4,-3,2,-13 +orthogroup_660_with_4_species.fasta,9,14,14,20 +orthogroup_623_with_4_species.fasta,10,17,16,17 +orthogroup_283_with_2_species.fasta,NaN,0,5,NaN +orthogroup_651_with_4_species.fasta,10,6,8,4 +orthogroup_368_with_4_species.fasta,16,8,-1,12 +orthogroup_343_with_4_species.fasta,-3,-8,0,-1 +orthogroup_301_with_4_species.fasta,12,9,9,16 +orthogroup_707_with_4_species.fasta,5,1,6,8 +orthogroup_113_with_4_species.fasta,16,1,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/GC_percent.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,0.00679245283019,NaN,0.00672955974843,NaN +orthogroup_544_with_4_species.fasta,0.00516949152542,0.00539548022599,0.00514124293785,0.0054802259887 +orthogroup_546_with_4_species.fasta,0.00625,0.00611111111111,0.00541666666667,0.00625 +orthogroup_761_with_4_species.fasta,0.00518763796909,0.00591611479029,0.00534216335541,0.00582781456954 +orthogroup_299_with_2_species.fasta,0.00484848484848,0.00598484848485,NaN,NaN +orthogroup_404_with_4_species.fasta,0.005,0.00566666666667,0.0055,0.00533333333333 +orthogroup_316_with_4_species.fasta,0.00553571428571,0.00583333333333,0.00575892857143,0.00566964285714 +orthogroup_487_with_4_species.fasta,0.00578947368421,0.00578947368421,0.00649122807018,0.00561403508772 +orthogroup_109_with_3_species.fasta,0.00537037037037,0.00524691358025,NaN,0.00598765432099 +orthogroup_696_with_4_species.fasta,0.00502222222222,0.00515555555556,0.0052,0.0056 +orthogroup_442_with_4_species.fasta,0.00455555555556,0.0045,0.00461111111111,0.00422222222222 +orthogroup_508_with_4_species.fasta,0.00545454545455,0.00537878787879,0.00492424242424,0.00560606060606 +orthogroup_588_with_4_species.fasta,0.00548854604956,0.00569892473118,0.00565684899486,0.00541841982235 +orthogroup_727_with_4_species.fasta,0.00575757575758,0.00583333333333,0.00477272727273,0.00515151515152 +orthogroup_335_with_4_species.fasta,0.00590717299578,0.00611814345992,0.00599156118143,0.00662447257384 +orthogroup_660_with_4_species.fasta,0.00525925925926,0.00503703703704,0.00503703703704,0.00474074074074 +orthogroup_623_with_4_species.fasta,0.00598290598291,0.00606837606838,0.00615384615385,0.00589743589744 +orthogroup_283_with_2_species.fasta,NaN,0.00352941176471,0.00401960784314,NaN +orthogroup_651_with_4_species.fasta,0.00588235294118,0.0056862745098,0.00509803921569,0.00549019607843 +orthogroup_368_with_4_species.fasta,0.00533333333333,0.00551111111111,0.00493333333333,0.00542222222222 +orthogroup_343_with_4_species.fasta,0.00560975609756,0.00585365853659,0.00552845528455,0.00626016260163 +orthogroup_301_with_4_species.fasta,0.00515151515152,0.0055303030303,0.0055303030303,0.00515151515152 +orthogroup_707_with_4_species.fasta,0.00583333333333,0.00561111111111,0.00533333333333,0.00611111111111 +orthogroup_113_with_4_species.fasta,0.00505952380952,0.00532738095238,0.00541666666667,0.00556547619048
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,-0.0188679245283,NaN,-0.0125786163522,NaN +orthogroup_544_with_4_species.fasta,0.0932203389831,0.104519774011,0.090395480226,0.0847457627119 +orthogroup_546_with_4_species.fasta,-0.0138888888889,0.0833333333333,0.0416666666667,0.0416666666667 +orthogroup_761_with_4_species.fasta,0.0353200883002,0.0286975717439,0.046357615894,0.0684326710817 +orthogroup_299_with_2_species.fasta,-0.0151515151515,-0.0530303030303,NaN,NaN +orthogroup_404_with_4_species.fasta,-0.266666666667,-0.233333333333,-0.25,-0.266666666667 +orthogroup_316_with_4_species.fasta,0.133928571429,0.136904761905,0.135416666667,0.129464285714 +orthogroup_487_with_4_species.fasta,-0.0350877192982,-0.0701754385965,-0.0350877192982,0.0526315789474 +orthogroup_109_with_3_species.fasta,-0.0185185185185,0.0432098765432,NaN,-0.0308641975309 +orthogroup_696_with_4_species.fasta,0.0533333333333,0.04,0.0888888888889,0.0311111111111 +orthogroup_442_with_4_species.fasta,0.111111111111,0.0833333333333,0.0944444444444,0.0444444444444 +orthogroup_508_with_4_species.fasta,-0.136363636364,-0.0984848484848,-0.159090909091,-0.106060606061 +orthogroup_588_with_4_species.fasta,0.00420757363254,0.00935016362786,-0.0070126227209,0.00280504908836 +orthogroup_727_with_4_species.fasta,0.0757575757576,0.0681818181818,0.0681818181818,0.0909090909091 +orthogroup_335_with_4_species.fasta,-0.0886075949367,-0.042194092827,-0.0210970464135,-0.0168776371308 +orthogroup_660_with_4_species.fasta,0.0296296296296,0.00740740740741,0.00740740740741,0.00740740740741 +orthogroup_623_with_4_species.fasta,0.00854700854701,0.0512820512821,-0.025641025641,0.017094017094 +orthogroup_283_with_2_species.fasta,NaN,-0.0196078431373,-0.0686274509804,NaN +orthogroup_651_with_4_species.fasta,0.0,0.0392156862745,0.0392156862745,0.0196078431373 +orthogroup_368_with_4_species.fasta,0.0133333333333,0.0577777777778,0.0355555555556,0.0488888888889 +orthogroup_343_with_4_species.fasta,0.0,0.0243902439024,0.00813008130081,-0.0487804878049 +orthogroup_301_with_4_species.fasta,0.106060606061,0.0984848484848,0.0681818181818,0.0454545454545 +orthogroup_707_with_4_species.fasta,-0.0388888888889,0.00555555555556,-0.0222222222222,-0.0111111111111 +orthogroup_113_with_4_species.fasta,0.0297619047619,0.0625,0.0654761904762,0.0863095238095
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,-18.8679245283,NaN,-12.5786163522,NaN +orthogroup_544_with_4_species.fasta,93.2203389831,104.519774011,90.395480226,84.7457627119 +orthogroup_546_with_4_species.fasta,-13.8888888889,83.3333333333,41.6666666667,41.6666666667 +orthogroup_761_with_4_species.fasta,35.3200883002,28.6975717439,46.357615894,68.4326710817 +orthogroup_299_with_2_species.fasta,-15.1515151515,-53.0303030303,NaN,NaN +orthogroup_404_with_4_species.fasta,-266.666666667,-233.333333333,-250.0,-266.666666667 +orthogroup_316_with_4_species.fasta,133.928571429,136.904761905,135.416666667,129.464285714 +orthogroup_487_with_4_species.fasta,-35.0877192982,-70.1754385965,-35.0877192982,52.6315789474 +orthogroup_109_with_3_species.fasta,-18.5185185185,43.2098765432,NaN,-30.8641975309 +orthogroup_696_with_4_species.fasta,53.3333333333,40.0,88.8888888889,31.1111111111 +orthogroup_442_with_4_species.fasta,111.111111111,83.3333333333,94.4444444444,44.4444444444 +orthogroup_508_with_4_species.fasta,-136.363636364,-98.4848484848,-159.090909091,-106.060606061 +orthogroup_588_with_4_species.fasta,4.20757363254,9.35016362786,-7.0126227209,2.80504908836 +orthogroup_727_with_4_species.fasta,75.7575757576,68.1818181818,68.1818181818,90.9090909091 +orthogroup_335_with_4_species.fasta,-88.6075949367,-42.194092827,-21.0970464135,-16.8776371308 +orthogroup_660_with_4_species.fasta,29.6296296296,7.40740740741,7.40740740741,7.40740740741 +orthogroup_623_with_4_species.fasta,8.54700854701,51.2820512821,-25.641025641,17.094017094 +orthogroup_283_with_2_species.fasta,NaN,-19.6078431373,-68.6274509804,NaN +orthogroup_651_with_4_species.fasta,0.0,39.2156862745,39.2156862745,19.6078431373 +orthogroup_368_with_4_species.fasta,13.3333333333,57.7777777778,35.5555555556,48.8888888889 +orthogroup_343_with_4_species.fasta,0.0,24.3902439024,8.13008130081,-48.7804878049 +orthogroup_301_with_4_species.fasta,106.060606061,98.4848484848,68.1818181818,45.4545454545 +orthogroup_707_with_4_species.fasta,-38.8888888889,5.55555555556,-22.2222222222,-11.1111111111 +orthogroup_113_with_4_species.fasta,29.7619047619,62.5,65.4761904762,86.3095238095
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,0.062893081761,NaN,0.0566037735849,NaN +orthogroup_544_with_4_species.fasta,0.0367231638418,0.0197740112994,0.0621468926554,0.0734463276836 +orthogroup_546_with_4_species.fasta,-0.0694444444444,-0.0555555555556,-0.263888888889,-0.152777777778 +orthogroup_761_with_4_species.fasta,-0.00662251655629,-0.0485651214128,-0.0176600441501,-0.0441501103753 +orthogroup_299_with_2_species.fasta,-0.030303030303,0.113636363636,NaN,NaN +orthogroup_404_with_4_species.fasta,-0.0333333333333,-0.0333333333333,-0.116666666667,0.0 +orthogroup_316_with_4_species.fasta,0.0386904761905,0.0386904761905,0.0133928571429,0.0520833333333 +orthogroup_487_with_4_species.fasta,0.0526315789474,0.0877192982456,0.122807017544,0.0350877192982 +orthogroup_109_with_3_species.fasta,0.0925925925926,0.104938271605,NaN,0.0925925925926 +orthogroup_696_with_4_species.fasta,-0.0311111111111,-0.0355555555556,-0.111111111111,-0.08 +orthogroup_442_with_4_species.fasta,-0.0444444444444,-0.00555555555556,-0.0722222222222,-0.0111111111111 +orthogroup_508_with_4_species.fasta,-0.121212121212,-0.113636363636,-0.0530303030303,-0.0757575757576 +orthogroup_588_with_4_species.fasta,-0.0233754090697,-0.0462833099579,-0.0476858345021,-0.0210378681627 +orthogroup_727_with_4_species.fasta,-0.0151515151515,0.0530303030303,0.0984848484848,0.0909090909091 +orthogroup_335_with_4_species.fasta,0.0168776371308,-0.0126582278481,0.0084388185654,-0.0548523206751 +orthogroup_660_with_4_species.fasta,0.0666666666667,0.103703703704,0.103703703704,0.148148148148 +orthogroup_623_with_4_species.fasta,0.0854700854701,0.145299145299,0.136752136752,0.145299145299 +orthogroup_283_with_2_species.fasta,NaN,0.0,0.0490196078431,NaN +orthogroup_651_with_4_species.fasta,0.0980392156863,0.0588235294118,0.078431372549,0.0392156862745 +orthogroup_368_with_4_species.fasta,0.0711111111111,0.0355555555556,-0.00444444444444,0.0533333333333 +orthogroup_343_with_4_species.fasta,-0.0243902439024,-0.0650406504065,0.0,-0.00813008130081 +orthogroup_301_with_4_species.fasta,0.0909090909091,0.0681818181818,0.0681818181818,0.121212121212 +orthogroup_707_with_4_species.fasta,0.0277777777778,0.00555555555556,0.0333333333333,0.0444444444444 +orthogroup_113_with_4_species.fasta,0.047619047619,0.00297619047619,0.0238095238095,0.0208333333333
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,62.893081761,NaN,56.6037735849,NaN +orthogroup_544_with_4_species.fasta,36.7231638418,19.7740112994,62.1468926554,73.4463276836 +orthogroup_546_with_4_species.fasta,-69.4444444444,-55.5555555556,-263.888888889,-152.777777778 +orthogroup_761_with_4_species.fasta,-6.62251655629,-48.5651214128,-17.6600441501,-44.1501103753 +orthogroup_299_with_2_species.fasta,-30.303030303,113.636363636,NaN,NaN +orthogroup_404_with_4_species.fasta,-33.3333333333,-33.3333333333,-116.666666667,0.0 +orthogroup_316_with_4_species.fasta,38.6904761905,38.6904761905,13.3928571429,52.0833333333 +orthogroup_487_with_4_species.fasta,52.6315789474,87.7192982456,122.807017544,35.0877192982 +orthogroup_109_with_3_species.fasta,92.5925925926,104.938271605,NaN,92.5925925926 +orthogroup_696_with_4_species.fasta,-31.1111111111,-35.5555555556,-111.111111111,-80.0 +orthogroup_442_with_4_species.fasta,-44.4444444444,-5.55555555556,-72.2222222222,-11.1111111111 +orthogroup_508_with_4_species.fasta,-121.212121212,-113.636363636,-53.0303030303,-75.7575757576 +orthogroup_588_with_4_species.fasta,-23.3754090697,-46.2833099579,-47.6858345021,-21.0378681627 +orthogroup_727_with_4_species.fasta,-15.1515151515,53.0303030303,98.4848484848,90.9090909091 +orthogroup_335_with_4_species.fasta,16.8776371308,-12.6582278481,8.4388185654,-54.8523206751 +orthogroup_660_with_4_species.fasta,66.6666666667,103.703703704,103.703703704,148.148148148 +orthogroup_623_with_4_species.fasta,85.4700854701,145.299145299,136.752136752,145.299145299 +orthogroup_283_with_2_species.fasta,NaN,0.0,49.0196078431,NaN +orthogroup_651_with_4_species.fasta,98.0392156863,58.8235294118,78.431372549,39.2156862745 +orthogroup_368_with_4_species.fasta,71.1111111111,35.5555555556,-4.44444444444,53.3333333333 +orthogroup_343_with_4_species.fasta,-24.3902439024,-65.0406504065,0.0,-8.13008130081 +orthogroup_301_with_4_species.fasta,90.9090909091,68.1818181818,68.1818181818,121.212121212 +orthogroup_707_with_4_species.fasta,27.7777777778,5.55555555556,33.3333333333,44.4444444444 +orthogroup_113_with_4_species.fasta,47.619047619,2.97619047619,23.8095238095,20.8333333333
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,0.00522012578616,NaN,0.00522012578616,NaN +orthogroup_544_with_4_species.fasta,0.00564971751412,0.00562146892655,0.00576271186441,0.00579096045198 +orthogroup_546_with_4_species.fasta,0.00458333333333,0.00513888888889,0.00388888888889,0.00444444444444 +orthogroup_761_with_4_species.fasta,0.00514348785872,0.00490066225166,0.00514348785872,0.00512141280353 +orthogroup_299_with_2_species.fasta,0.00477272727273,0.00530303030303,NaN,NaN +orthogroup_404_with_4_species.fasta,0.0035,0.00366666666667,0.00316666666667,0.00366666666667 +orthogroup_316_with_4_species.fasta,0.0058630952381,0.00587797619048,0.00574404761905,0.00590773809524 +orthogroup_487_with_4_species.fasta,0.00508771929825,0.00508771929825,0.00543859649123,0.00543859649123 +orthogroup_109_with_3_species.fasta,0.00537037037037,0.00574074074074,NaN,0.00530864197531 +orthogroup_696_with_4_species.fasta,0.00511111111111,0.00502222222222,0.00488888888889,0.00475555555556 +orthogroup_442_with_4_species.fasta,0.00533333333333,0.00538888888889,0.00511111111111,0.00516666666667 +orthogroup_508_with_4_species.fasta,0.00371212121212,0.00393939393939,0.00393939393939,0.00409090909091 +orthogroup_588_with_4_species.fasta,0.00490416082281,0.00481533426835,0.00472650771388,0.00490883590463 +orthogroup_727_with_4_species.fasta,0.00530303030303,0.00560606060606,0.00583333333333,0.00590909090909 +orthogroup_335_with_4_species.fasta,0.00464135021097,0.00472573839662,0.00493670886076,0.00464135021097 +orthogroup_660_with_4_species.fasta,0.00548148148148,0.00555555555556,0.00555555555556,0.00577777777778 +orthogroup_623_with_4_species.fasta,0.00547008547009,0.00598290598291,0.00555555555556,0.00581196581197 +orthogroup_283_with_2_species.fasta,NaN,0.00490196078431,0.00490196078431,NaN +orthogroup_651_with_4_species.fasta,0.00549019607843,0.00549019607843,0.00558823529412,0.00529411764706 +orthogroup_368_with_4_species.fasta,0.00542222222222,0.00546666666667,0.00515555555556,0.00551111111111 +orthogroup_343_with_4_species.fasta,0.00487804878049,0.00479674796748,0.0050406504065,0.00471544715447 +orthogroup_301_with_4_species.fasta,0.00598484848485,0.00583333333333,0.00568181818182,0.00583333333333 +orthogroup_707_with_4_species.fasta,0.00494444444444,0.00505555555556,0.00505555555556,0.00516666666667 +orthogroup_113_with_4_species.fasta,0.0053869047619,0.00532738095238,0.00544642857143,0.00553571428571
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/A.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,24,NaN,25,NaN +orthogroup_544_with_4_species.fasta,102,100,102,95 +orthogroup_546_with_4_species.fasta,13,17,18,15 +orthogroup_761_with_4_species.fasta,117,99,116,110 +orthogroup_299_with_2_species.fasta,33,23,NaN,NaN +orthogroup_404_with_4_species.fasta,7,6,6,6 +orthogroup_316_with_4_species.fasta,195,186,188,189 +orthogroup_487_with_4_species.fasta,11,10,9,14 +orthogroup_109_with_3_species.fasta,36,42,NaN,30 +orthogroup_696_with_4_species.fasta,62,59,64,53 +orthogroup_442_with_4_species.fasta,59,57,57,56 +orthogroup_508_with_4_species.fasta,21,24,23,22 +orthogroup_588_with_4_species.fasta,487,470,457,493 +orthogroup_727_with_4_species.fasta,33,32,39,38 +orthogroup_335_with_4_species.fasta,38,41,45,38 +orthogroup_660_with_4_species.fasta,34,34,34,36 +orthogroup_623_with_4_species.fasta,24,26,21,25 +orthogroup_283_with_2_species.fasta,NaN,32,27,NaN +orthogroup_651_with_4_species.fasta,21,24,27,24 +orthogroup_368_with_4_species.fasta,54,57,61,57 +orthogroup_343_with_4_species.fasta,27,27,28,20 +orthogroup_301_with_4_species.fasta,39,36,34,35 +orthogroup_707_with_4_species.fasta,34,40,40,34 +orthogroup_113_with_4_species.fasta,88,89,88,89
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/C.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,49,NaN,49,NaN +orthogroup_544_with_4_species.fasta,85,92,80,84 +orthogroup_546_with_4_species.fasta,25,24,29,28 +orthogroup_761_with_4_species.fasta,119,145,125,142 +orthogroup_299_with_2_species.fasta,34,32,NaN,NaN +orthogroup_404_with_4_species.fasta,16,18,20,16 +orthogroup_316_with_4_species.fasta,173,183,189,173 +orthogroup_487_with_4_species.fasta,15,14,15,15 +orthogroup_109_with_3_species.fasta,36,34,NaN,41 +orthogroup_696_with_4_species.fasta,60,62,71,72 +orthogroup_442_with_4_species.fasta,45,41,48,39 +orthogroup_508_with_4_species.fasta,44,43,36,42 +orthogroup_588_with_4_species.fasta,612,659,656,602 +orthogroup_727_with_4_species.fasta,39,35,25,28 +orthogroup_335_with_4_species.fasta,68,74,70,85 +orthogroup_660_with_4_species.fasta,31,27,27,22 +orthogroup_623_with_4_species.fasta,30,27,28,26 +orthogroup_283_with_2_species.fasta,NaN,18,18,NaN +orthogroup_651_with_4_species.fasta,25,26,22,26 +orthogroup_368_with_4_species.fasta,52,58,56,55 +orthogroup_343_with_4_species.fasta,36,40,34,39 +orthogroup_301_with_4_species.fasta,28,32,32,26 +orthogroup_707_with_4_species.fasta,50,50,45,51 +orthogroup_113_with_4_species.fasta,77,89,87,90
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/G.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,59,NaN,58,NaN +orthogroup_544_with_4_species.fasta,98,99,102,110 +orthogroup_546_with_4_species.fasta,20,20,10,17 +orthogroup_761_with_4_species.fasta,116,123,117,122 +orthogroup_299_with_2_species.fasta,30,47,NaN,NaN +orthogroup_404_with_4_species.fasta,14,16,13,16 +orthogroup_316_with_4_species.fasta,199,209,198,208 +orthogroup_487_with_4_species.fasta,18,19,22,17 +orthogroup_109_with_3_species.fasta,51,51,NaN,56 +orthogroup_696_with_4_species.fasta,53,54,46,54 +orthogroup_442_with_4_species.fasta,37,40,35,37 +orthogroup_508_with_4_species.fasta,28,28,29,32 +orthogroup_588_with_4_species.fasta,562,560,554,557 +orthogroup_727_with_4_species.fasta,37,42,38,40 +orthogroup_335_with_4_species.fasta,72,71,72,72 +orthogroup_660_with_4_species.fasta,40,41,41,42 +orthogroup_623_with_4_species.fasta,40,44,44,43 +orthogroup_283_with_2_species.fasta,NaN,18,23,NaN +orthogroup_651_with_4_species.fasta,35,32,30,30 +orthogroup_368_with_4_species.fasta,68,66,55,67 +orthogroup_343_with_4_species.fasta,33,32,34,38 +orthogroup_301_with_4_species.fasta,40,41,41,42 +orthogroup_707_with_4_species.fasta,55,51,51,59 +orthogroup_113_with_4_species.fasta,93,90,95,97
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/T.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,27,NaN,27,NaN +orthogroup_544_with_4_species.fasta,69,63,70,65 +orthogroup_546_with_4_species.fasta,14,11,15,12 +orthogroup_761_with_4_species.fasta,101,86,95,79 +orthogroup_299_with_2_species.fasta,35,30,NaN,NaN +orthogroup_404_with_4_species.fasta,23,20,21,22 +orthogroup_316_with_4_species.fasta,105,94,97,102 +orthogroup_487_with_4_species.fasta,13,14,11,11 +orthogroup_109_with_3_species.fasta,39,35,NaN,35 +orthogroup_696_with_4_species.fasta,50,50,44,46 +orthogroup_442_with_4_species.fasta,39,42,40,48 +orthogroup_508_with_4_species.fasta,39,37,44,36 +orthogroup_588_with_4_species.fasta,478,450,472,487 +orthogroup_727_with_4_species.fasta,23,23,30,26 +orthogroup_335_with_4_species.fasta,59,51,50,42 +orthogroup_660_with_4_species.fasta,30,33,33,35 +orthogroup_623_with_4_species.fasta,23,20,24,23 +orthogroup_283_with_2_species.fasta,NaN,34,34,NaN +orthogroup_651_with_4_species.fasta,21,20,23,22 +orthogroup_368_with_4_species.fasta,51,44,53,46 +orthogroup_343_with_4_species.fasta,27,24,27,26 +orthogroup_301_with_4_species.fasta,25,23,25,29 +orthogroup_707_with_4_species.fasta,41,39,44,36 +orthogroup_113_with_4_species.fasta,78,68,66,60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,11,4,5 +"Lower",7,4,5,7 +"Difference",-2,7,-1,-2 +"Trial_Number",12,15,9,12 +"p-value",0.7744140625,0.11846923828125,1,0.7744140625 +"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667 +"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843 +"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,3,6,10 +"Lower",7,7,7,5 +"Difference",0,-4,-1,5 +"Trial_Number",14,10,13,15 +"p-value",1,0.34375,1,0.3017578125 +"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667 +"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154 +"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/GC_percent.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",3,7,5,7 +"Lower",6,2,8,7 +"Difference",-3,5,-3,0 +"Trial_Number",9,9,13,14 +"p-value",0.5078125,0.1796875,0.5810546875,1 +"probability_of_success",0.333333333333333,0.777777777777778,0.384615384615385,0.5 +"confidence_interval_low",0.0748546314196918,0.399906426283688,0.138579338890161,0.230360541448062 +"confidence_interval_high",0.70070494379146,0.971855026522102,0.684222397085937,0.769639458551938
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,11,4,5 +"Lower",7,4,5,7 +"Difference",-2,7,-1,-2 +"Trial_Number",12,15,9,12 +"p-value",0.7744140625,0.11846923828125,1,0.7744140625 +"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667 +"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843 +"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,11,4,5 +"Lower",7,4,5,7 +"Difference",-2,7,-1,-2 +"Trial_Number",12,15,9,12 +"p-value",0.7744140625,0.11846923828125,1,0.7744140625 +"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667 +"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843 +"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,3,6,10 +"Lower",7,7,7,5 +"Difference",0,-4,-1,5 +"Trial_Number",14,10,13,15 +"p-value",1,0.34375,1,0.3017578125 +"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667 +"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154 +"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,3,6,10 +"Lower",7,7,7,5 +"Difference",0,-4,-1,5 +"Trial_Number",14,10,13,15 +"p-value",1,0.34375,1,0.3017578125 +"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667 +"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154 +"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/purine_percent.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",4,4,7,10 +"Lower",8,5,8,5 +"Difference",-4,-1,-1,5 +"Trial_Number",12,9,15,15 +"p-value",0.3876953125,1,1,0.3017578125 +"probability_of_success",0.333333333333333,0.444444444444444,0.466666666666667,0.666666666666667 +"confidence_interval_low",0.0992460911495833,0.136995662265167,0.212666729519308,0.383803732541154 +"confidence_interval_high",0.651124493581186,0.787991493221132,0.734138652722603,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/A.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,3,7,4 +"Lower",5,3,4,5 +"Difference",0,0,3,-1 +"Trial_Number",10,6,11,9 +"p-value",1,1,0.548828125,1 +"probability_of_success",0.5,0.5,0.636363636363636,0.444444444444444 +"confidence_interval_low",0.187086028447399,0.118117248757025,0.307904715011677,0.136995662265167 +"confidence_interval_high",0.812913971552601,0.881882751242975,0.890736556180902,0.787991493221132
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/C.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,7,5,5 +"Lower",6,3,6,8 +"Difference",-1,4,-1,-3 +"Trial_Number",11,10,11,13 +"p-value",1,0.34375,1,0.5810546875 +"probability_of_success",0.454545454545455,0.7,0.454545454545455,0.384615384615385 +"confidence_interval_low",0.167488094063707,0.347547149940003,0.167488094063707,0.138579338890161 +"confidence_interval_high",0.766206402340655,0.933260488822266,0.766206402340655,0.684222397085937
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/G.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",4,7,5,7 +"Lower",9,5,8,4 +"Difference",-5,2,-3,3 +"Trial_Number",13,12,13,11 +"p-value",0.266845703125,0.7744140625,0.5810546875,0.548828125 +"probability_of_success",0.307692307692308,0.583333333333333,0.384615384615385,0.636363636363636 +"confidence_interval_low",0.0909203945720966,0.276669685682106,0.138579338890161,0.307904715011677 +"confidence_interval_high",0.614261661750705,0.84834777019157,0.684222397085937,0.890736556180902
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/T.csv Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,4,8,6 +"Lower",4,11,4,7 +"Difference",3,-7,4,-1 +"Trial_Number",11,15,12,13 +"p-value",0.548828125,0.11846923828125,0.3876953125,1 +"probability_of_success",0.636363636363636,0.266666666666667,0.666666666666667,0.461538461538462 +"confidence_interval_low",0.307904715011677,0.0778715462910436,0.348875506418814,0.192232441801288 +"confidence_interval_high",0.890736556180902,0.551003241036971,0.900753908850417,0.748654517729696
--- a/test-data/OUT_nuc/Purine_Load_Indice.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_TOTAL,Ac_DIFF_GC,Ac_DIFF_AT,Ac_PLI_GC1000,Ac_PLI_AT1000,Pu_TOTAL,Pu_DIFF_GC,Pu_DIFF_AT,Pu_PLI_GC1000,Pu_PLI_AT1000,Am_TOTAL,Am_DIFF_GC,Am_DIFF_AT,Am_PLI_GC1000,Am_PLI_AT1000,Ap_TOTAL,Ap_DIFF_GC,Ap_DIFF_AT,Ap_PLI_GC1000,Ap_PLI_AT1000,Pf_TOTAL,Pf_DIFF_GC,Pf_DIFF_AT,Pf_PLI_GC1000,Pf_PLI_AT1000,Pg_TOTAL,Pg_DIFF_GC,Pg_DIFF_AT,Pg_PLI_GC1000,Pg_PLI_AT1000,Ph_TOTAL,Ph_DIFF_GC,Ph_DIFF_AT,Ph_PLI_GC1000,Ph_PLI_AT1000,Ps_TOTAL,Ps_DIFF_GC,Ps_DIFF_AT,Ps_PLI_GC1000,Ps_PLI_AT1000,Pp_TOTAL,Pp_DIFF_GC,Pp_DIFF_AT,Pp_PLI_GC1000,Pp_PLI_AT1000,Pa_TOTAL,Pa_DIFF_GC,Pa_DIFF_AT,Pa_PLI_GC1000,Pa_PLI_AT1000 -locus1_sp8_sp8.fasta,198,6,20,30.30303,101.01010,231,4,19,17.31602,82.25108,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,231,6,21,25.97403,90.90909,231,15,8,64.93506,34.63203,231,19,10,82.25108,43.29004,0,0,0,0.00000,0.00000,198,10,14,50.50505,70.70707,231,13,10,56.27706,43.29004 -locus1_sp6_sp6.fasta,234,2,28,8.54701,119.65812,234,6,20,25.64103,85.47009,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,234,18,20,76.92308,85.47009,234,0,24,0.00000,102.56410,234,8,16,34.18803,68.37607,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,234,-1,23,-4.27350,98.29060 -locus2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,NA,NA,NA,NA,NA,192,11,11,57.29167,57.29167,NA,NA,NA,NA,NA,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,192,14,12,72.91667,62.50000
--- a/test-data/OUT_nuc/nuc_compositions.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_prop_A,Ac_prop_T,Ac_prop_C,Ac_prop_G,Pu_prop_A,Pu_prop_T,Pu_prop_C,Pu_prop_G,Am_prop_A,Am_prop_T,Am_prop_C,Am_prop_G,Ap_prop_A,Ap_prop_T,Ap_prop_C,Ap_prop_G,Pf_prop_A,Pf_prop_T,Pf_prop_C,Pf_prop_G,Pg_prop_A,Pg_prop_T,Pg_prop_C,Pg_prop_G,Ph_prop_A,Ph_prop_T,Ph_prop_C,Ph_prop_G,Ps_prop_A,Ps_prop_T,Ps_prop_C,Ps_prop_G,Pp_prop_A,Pp_prop_T,Pp_prop_C,Pp_prop_G,Pa_prop_A,Pa_prop_T,Pa_prop_C,Pa_prop_G -locus1_sp8_sp8.fasta,0.33333,0.23232,0.20202,0.23232,0.32468,0.24242,0.20779,0.22511,NA,NA,NA,NA,NA,NA,NA,NA,0.32900,0.23810,0.20346,0.22944,0.29437,0.25974,0.19048,0.25541,0.32035,0.27706,0.16017,0.24242,0.00000,0.00000,0.00000,0.00000,0.34343,0.27273,0.16667,0.21717,0.29870,0.25541,0.19481,0.25108 -locus1_sp6_sp6.fasta,0.33761,0.21795,0.21795,0.22650,0.28632,0.20085,0.24359,0.26923,NA,NA,NA,NA,NA,NA,NA,NA,0.29915,0.21368,0.20513,0.28205,0.31624,0.21368,0.23504,0.23504,0.30342,0.23504,0.21368,0.24786,NA,NA,NA,NA,NA,NA,NA,NA,0.31624,0.21795,0.23504,0.23077 -locus2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,NA,NA,NA,NA,0.30208,0.24479,0.19792,0.25521,NA,NA,NA,NA,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,NA,NA,NA,NA,NA,NA,NA,NA,0.31771,0.25521,0.17708,0.25000
--- a/test-data/OUT_nuc/percent_GC.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_percent_GC,Pu_percent_GC,Am_percent_GC,Ap_percent_GC,Pf_percent_GC,Pg_percent_GC,Ph_percent_GC,Ps_percent_GC,Pp_percent_GC,Pa_percentGC -locus1_sp8_sp8.fasta,43.43434,43.29004,NA,NA,43.29004,44.58874,40.25974,0.00000,38.38384,44.58874 -locus1_sp6_sp6.fasta,44.44444,51.28205,NA,NA,48.71795,47.00855,46.15385,NA,NA,46.58120 -locus2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833
--- a/test-data/OUT_nuc/percent_purine.csv Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -LOCUS,Ac_percent_purine,Pu_percent_purine,Am_percent_purine,Ap_percent_purine,Pf_percent_purine,Pg_percent_purine,Ph_percent_purine,Ps_percent_purine,Pp_percent_purine,Pa_percent_purine -locus1_sp8_sp8.fasta,56.56566,54.97835,NA,NA,55.84416,54.97835,56.27706,0.00000,56.06061,54.97835 -locus1_sp6_sp6.fasta,56.41026,55.55556,NA,NA,58.11966,55.12821,55.12821,NA,NA,54.70085 -locus2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_3sp_2.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,6 @@ +>Pg1Pg2_ContigI_295 +YGLYKQATVGEINTDRPGMLDFKGKAKWDAWE +>Pp_2630_2/3_0.667_949 +YGLYKQVTVGDVNAARPGMLDFKGKAKWDAWE +>Ap3661_1/2_1.000_1488 +YGLYKQATVGDVNTDRPGMLDFKGKAKWDAWE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_3sp_7.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,6 @@ +>Ac10784_3/3_0.600_925 +DLRSNLSNYKLQLQQVEAALALDQENEDLKKLQKD +>Pf1355_1/1_1.000_940 +DLRTNLSNYKLQLQQVEAALALDQENEDLKKLQKD +>Ap11551_1/2_1.000_2287 +DLRSNLSNYKLQLQQVEAALALDQDNEDLKKLQKD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_4sp_4.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Pg1Pg2_ContigI_830 +RHVECFTCSMRKFILFGTILPPTRLLTITPTACVTLYTRSLAMIIFVWHTFLDCSITLYIHNVTNFINFHIS +>Pf879_1/1_1.000_626 +RHLECLTCSIRKFILLGMILPPTRLFTITPTACVTLYTRCLAMVIFVRHTFLDCSITLYIYDITNFIHFHVS +>Ac197_2/2_1.000_643 +RHFECLTCSIRKLILLAMILPPTRLLTITPTACVTLYTRSLAMVVFVRHTFLDSSISLNIHYVTHFVHFHIG +>Pp_589_1/1_1.000_552 +LHFECFMCSIRRLILFGMILPPTRLLTITPTACVTLYIRCLAMVIFMRHSFLDCTMTLDIHNIPYFVHFHIR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_4sp_6.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Pg1Pg2_ContigI_1514 +PGLCLECYTCVRQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWKPHGDRIHFINKGCMRYERCLDWQVSKRHTCRRDWYLDWECVECCRGDMC +>Ap3180_1/2_1.000_1116 +PGLCLECYTCVNQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWRPHGDRIHFINKGCMRFEKCLDWQVARRHTCRRDWYLDWECIECCRGDMC +>Ac2018_1/1_1.000_627 +PGLCLECYTCVNQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWRPHGDRIHFINKGCMRFERCLDWQKSRRNTCRRDWYLDWECVECCRGDMC +>Pf2190_1/1_1.000_917 +PGLCLECYTCVRQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWKPHGDRIYFINKGCMRFEKCLEWQKLKRHTCRRDWYLDWECVECCRGDMC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_10.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Ap5723_1/1_1.000_1183 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA +>Ac8933_1/2_1.000_1159 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA +>PsIsotig20888_13433_1513 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPLA +>Pp_2523_1/1_1.000_2145 +CFNGYEHTSDYVGKAYFGCWWIFHKEYSYVRDWIMPSWFIACQTLMTFAIVTMFITLGLFPMA +>Pg1Pg2_ContigI_6331 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA +>Pf1268_1/1_1.000_688 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPLA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_11.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>PsContig23463_00014_509 +GDDAAQKQEILDWIEAVTGSKIPRDQPFEKILKDGVILCNLMNKIMPGSVKRINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGFDGPTIGPKMAEKQEREWTEDQLREGRQGIIGLQAG +>Pf344_1/1_1.000_2337 +GDDAAQKQEILDWIEAVIGSKIPRDQPFEKILKDGVILCNLMNKIMPGSVKRINKKGGNFALMENIAAFQKAMKDYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGFDGPTIGPKMAEKHEREWTEDQLREGRQGIIGLQAG +>Pg1Pg2_ContigI_5539 +VDDAAQKQELLDWIEAVSGSKIPRDQRFEKILKDGVILCNMMNKIVPGSVKRINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGYDGPTIGPKMAEKHEREWTEDELREGRQGIIGLQAG +>Pp_115_7/8_0.421_2349 +GDDAAQKTEILDWIEAVTGTKIPRDQPFEKILKDGVILCNLMNKITPGSVKRINKKGGNFALMENIAAFQKAMKSYGVPEEEVFQTADLFEARNVKAVVKSLNALGRTCLNKGFDGPSFGPKMAEKHERQWTEDELREGRQGIIGLQAG +>Ac261_5/5_0.871_1061 +GDDAAQKQEILDWIEAVTGDKIPRDQPFEKVLKDGVILCNLMNKIMPGSVKKINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLAKGFDGPTIGPKMAEKQEREWTEDQLREGRQGIIGLQAG +>Ap77_5/8_0.405_866 +GDDAAQKQEILDWIEAVTGDKIPRDQPFEKVLKDGVILCNLINKIMPGSVKKINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLAKGFDGPTIGPKMAEKHEREWTEDQLREGRQGIIGLQAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_16.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Ap3513_1/1_1.000_737 +KIGTVGISHYAQEALGDIVFAELPEVGSEFVKDDECGTLESV +>Pp_7121_2/3_0.778_2103 +KIGTIGISHYAQEALGDIVFAELPEDGAEFDKDDECGTLESV +>Pg1Pg2_ContigI_3765 +KIGTIGISHYAQEALGDIVYAELPEVGSEFNKFDECGTLESV +>Pf199_1/1_1.000_306 +KIGTVGISQYAQEALGDIVYAELPDVGSEFNKHDECGTLESV +>Ac4439_1/1_1.000_890 +KIGTVGISHYAQEALGDIVFAELPEAGSEFVKDDECGTLESV +>PsIsotig06983_01306_1511 +KIGTVGISQYAQEALGDIVYAELPDVGSEFTKHDECGTLESV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_18.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Ac3728_1/2_1.000_2558 +AMLHLMLPGTVITYYGEEIGM +>Pp_1484_1/1_1.000_2519 +AMVHLMLPGTAITYYGEEIGM +>Ap459_1/1_1.000_2245 +AMLHLMLPGTAITYYGEEIGM +>Pf737_1/1_1.000_940 +AMLHLLLPGTAITYYGEEIGM +>Pg1Pg2_ContigI_2873 +AMLHLMLPGTAITYYGEEIGM +>PsContig14622_00221_1814 +AMLHLMLPGTAITYYGEEIGM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_25.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pg1Pg2_ContigI_440 +DGGGNLLVAADSYIGEKIRDLAVECGIEFDEEGTSVIDHHNYDVNDDGKHTLIVADPDNLVTAPLLTGSETHNPLLFKGVGMTADPDNPLVISILHASSSSYSFDPNSPITDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKASGGKKYAKSGNQQLALRLSQWVFKEKGVLRVGKVTHHKKGEKEPPVAYTIMDTVEYTIEIEQFEDGKWMPLVADDVQLEFVRIDPFVRMGLRKKGGKFYAKFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLEHTQYE +>Pf3990_1/1_1.000_914 +DGGGNLLVAADSYIGETIRDLAVECGVEFDEEGTAVIDHHNYDVKDDGKHTLIVADPENLVNAPVLTGTEKHNPLLFKGVGMTADPDNPLVISILHASSSAYSFDPDSRINDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKAGGGQKYAKSANQELATRLSQWVFKEKGVLRVGKVTHHRKGEKEPPVAYTIMDTVEYTIEIEKKEGDKWLPLDANDVQLEFVRIDPFIRMGLRKKGGKFHAEFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLQHTQYE +>Pp_205_1/1_1.000_1576 +DGGGNVLVAADSYIGETIRDLAGECGVEFDEEGTSVIDHLNYDVKDNGKHTLIVANPDNLVNAPMLIGSEKHNPLLFKGVGMTADPDNPLVINILHAASSAYSFDPDSRIQDYPHAVGKNTLLIAGLQARNNARVLFFGSLDFFSDETFNAPVQKSGTTQKYSKSGNQHLALRLSQWVFKEKGVLRVGKVVHHKEGEKEPPMAYTVMDIVEYSVEIEKNEDGKWMPLDAKDVQLEFVRIDPFVRMALTKKGNKFYAKFKIPDVYGVYQFRVDYNRIGYTHLFITTQVSVRPLQHTQYE +>Ap3808_1/1_1.000_2053 +DGGGNVLVAVDSYIGETIRNLAGECGVEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLINAPLLTGNEKHNPLLFRGVGMTADPDNPLVINILHAASSAYSFDPDSRITDYPHAIGKNTLLISGLQARNNARVLFVGSLDFFSDETFNAPVQKANGGQKFSKSGNQQLATRLSQWVFKEKGVLRVGKVVHHKVGEKEPPAAYTIMDNVEYSVEIEKNEDGKWVPLDADDLQLEFVRIDPFIRMPLSKRGNQFYAKFKIPDVYGVYQFRVDYNRVGYTHLFITTQVSVRPLEHTQYE +>Ac3918_1/1_1.000_1754 +DGGGNVLVAVDSYIGETIRNLAGECGVEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLINAPLLTGSEKHAPLLFRGVGMTADPDNPLVINILHAASSAYSFDPDSRITDYPHAVGKNTLLISGLQARNNARVLFVGSLDFFSDETFNAPVQKANGGQKFPKSGNQQLATRLSQWVFKEKGVLRVGKVVHHKVGEKEPPAAYTIMDNVEYSVEIEKNEDGKWLPLDADDLQLEFVRIDPFIRMPLTKKGNQFYAKFKIPDVYGVYQFRIDYNRIGYTHLFITTQVSVRPLEHTQYE +>PsIsotig14896_07441_3814 +DGGGNLLVAADSFIGETIRDLAVECGIEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLVSAPMLTGTEKHNPLLFKGVGMTADPDNPLVISILHASSSAYSFDPNSRITDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKAGGGLRYAKSGNQLLALRLSQWVFKEKGVLRVGKVTHHKKGEKVPPVAYTIMDTVEYTIEIEKNEDGKWVPLDADDVQLEFVRIDPFVRMGLHKKGDKFYAEFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLEHTQYE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_27.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pf1236_1/1_1.000_402 +LLWSEILRLVPFTSVELAQVRLLRLVHHCHDPC +>PsIsotig05584_00818_503 +LLRSQILWLVLFTSVKLPQIGFLCLVHHRHDPC +>Pp_3399_1/1_1.000_348 +LLWSQILRLVFLIFVELAQILLLRLVHHCQYTG +>Ac363_1/1_1.000_432 +LLSPQVLWLVLFTFVKLAQVFLLCLVHHRHDSG +>Pg1Pg2_ContigI_2596 +LLRSQVLWLVLFTTIKLSQVVLLCLMHHRHDSC +>Ap1830_1/1_1.000_511 +LLSPQVLWLVLFTFVKLAQVFLLCLVHHCHDSG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_30.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pf1581_1/1_1.000_1837 +NWAVFENDMKWKPMEKRK +>Pp_1355_1/1_1.000_1833 +NWAVFENDMKWKPMEKRE +>Ac1659_1/1_1.000_1848 +NWAVFENDMKWKPMEKRK +>Pg1Pg2_ContigI_3242 +NWAVFENDMKWKPMEKRK +>PsIsotig07835_01762_1971 +NWAVFENDMKWRPMEKRK +>Ap3485_1/1_1.000_1864 +NWAVFENDMKWKPMEKRK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_32.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>PsIsotig12291_04836_2510 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFEAELYQSEYTIEDEQLKALLATSASRKAAKKKKK +>Pf61_1/1_1.000_1008 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFEADLYQSEHTIEDEQLKALLATSASRKAAKKKKK +>Ac1652_1/1_1.000_2305 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMRITGLPLDLDIYQSEYKIEDEQIKSILATSASRKAAKKKKK +>Ap914_1/1_1.000_2326 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMRITGLPLDLDLYKSEYKIEDEQIKSILATSASRKAAKKKKK +>Pg1Pg2_ContigI_2687 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFETEIYESEHTIDDEELKTLLATSASRKAAKKKKK +>Pp_3975_1/1_1.000_1535 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMMITGLPFDPDLYQSEYSVEDEKLKGLLAMSASRKAAKKKKK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_35.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>PsIsotig06251_01036_1545 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVTCGFSGFCLHGFWCLVFIVMGWHLC +>Ac7666_1/1_1.000_1396 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSTKFTRDLFKVACGPCCFCLHGIWSVVLVTLGWNLC +>Pg1Pg2_ContigI_275 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVTCGSSGICIYGIRCLVPIVVGWHLC +>Ap4162_1/1_1.000_589 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSTKFTRDLFKVACGPCCFCLHGIWSVVLITLGWNLC +>Pp_3408_2/2_1.000_676 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSSKFTRDLFKVTRGTSSFCIHGIWCIISLAVGWNLC +>Pf3031_1/1_1.000_540 +SRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVARSFSGFCLHGLWCIVLVVMGWYLR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_38.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pf4498_1/1_1.000_1098 +FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSASPQHSPPAKYSKKEARDNNKYYSKEYENHYDRDYHHRDSRHEHERSKHKRRRHTPTYSPVRSYSRSPEPRSKAHKKYYKEKYRA +>Pg1Pg2_Pg13774_1/1_1.000_1948 +FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSASPQHSPPAKYSKKEARDNNKYYSKDYENHYDRDYHHRDSRHDHERSKHKRRRHTPTYSPVRSYSRSPEPRSKTHKKYYKEKYRA +>Pp_3267_1/2_1.000_1460 +FVGGTRKKRSRSRTRSNSKSRSYSSQESNSTGSPQRSPPVKFSKKEARDNNKYYSKEYDNHYDRDYHHRDSHRDHERSKHKRRRHTPTYSPIRSYSRSPEPRSKTHKKYYKEKYRA +>Ac4272_1/2_1.000_2412 +FGGGSRKKRSRSHTRSNSKPRSYSSQESNSTASPQHSPPAKYSKKEARDNNKYYSKEYDNHYERDYHHRDSHHDHERSKHKRRRHTPTYSPLRSYSRSPEPRSKTHKKYYKEKYRA +>Ap3418_1/1_1.000_1919 +FGGGSRKKRSRSHTRSNSKTRSYSSQESNSTASPQHSPPAKYSKKEARDNNKYYSKEYDNHYERDYHHRDSHHDHERSKHKRRRHTPTYSPLRSYSRSPEPRSKTHKKYYKEKYRA +>PsIsotig12297_04842_646 +FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSVSPHRSPPVKYSKKEARDNNKYYSKEYENHYDRDYHHRDSRHDHERSKHKRRRHTPTYSPVRSYSRSPEPRSKAHKKYYKEKYRA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_39.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>PsIsotig10643_03194_2284 +ITHVLNITAHVPFHFEAEGIVYKRLPATDSGHQNLKQYFEDAFKFIEERFRR +>Pp_6073_1/1_1.000_1725 +ITHVLNVTGHVPLHFEAQGIIYKRLPATDSGQQNLKQYFEDAFKFIEEKLWR +>Pf4635_1/1_1.000_231 +ITHVLNITAHVPFHFEAEGIVYKRLPATDSGHQNLKQYFEDAFRFIEERFKR +>Ac2807_1/1_1.000_2307 +ITHVLNVTAHVPFHFEEQGIIYKRLPATDSGHQNLKQYFEDAFTYIEEKFKW +>Pg1Pg2_ContigI_3109 +ITHVLNVTSHMPFHFEAQGITYKRLPATDSGHQNLKQYFEDAFKFIEETFRR +>Ap5088_1/1_1.000_2170 +ITHVLNVTAHVPFHFEEQGIKYKRLPATDSGHQNLKQYFQDAFTFIEETFRW
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_40.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Ac1381_1/2_1.000_1229 +MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTSQMEKNLMRKLKKKGIPGKFIARGGGKPGEAIISAADDEDADMIVMATRGRGRLMRVLLGSVS +>Pp_1351_1/1_1.000_1516 +MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTAQMEKALMRKLKIKGTPGKFITRGGGKPGEAILSAADDEDVDMIIMATRGRGKLMRVLLGSVS +>Ap2493_1/2_1.000_1233 +MHSFELPLMHSYEEMYVSPDMWQATLKKEAERTSQMEKNVMRRLKKKGIPGKFIARGGGKPGEAIVSAADDEDVDMIVMATRGRGRLMRVLLGSVS +>PsIsotig15400_07945_928 +MHCFELPLMHSYEEMYVSPEMWQATLKKEADRTSHMEKALMKKLKIKGIPGKFIARGGGKPGEAILSAAEDENVDMVVMGTRGRGKLMRVLLGSVS +>Pf1400_1/1_1.000_761 +MHCFELPLMHSYEEMYVSPEMWQATLKKEADKTAQMEKTLMRKLKIKGISGKFIARGGGKPGEAILSAAEDEDVDMIVMGTRGRGKLMRVLLGSVS +>Pg1Pg2_ContigI_142 +MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTTHMEKVLMKKLKLKGVPGKFIARGGGKPGEAILSAAEDENVDMIVMGTRGRGKLMRVLLGSVS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_41.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pf645_1/1_1.000_1413 +NSDLDTMTALGSRIRWITRRLGFLSRRVSTTSIVARTVFVALKSAFLQNSPSICSQGLAFSRTICMHVE +>Pg1Pg2_ContigI_3539 +NSDLDTITALGSRIRWITRRLGFLSRSVSTTSIVARTVFVALKSAFLQNSPSICSQGFAFSRTICMHVE +>Ap5964_2/2_1.000_2574 +NSDLDTMTALGSRIKWMTRRLGFLSSSVSTTSIVARTVFVALKSAFLQNSPSICSHGLAFSRTICIQVE +>Pp_3400_2/2_1.000_2104 +NSDLDTMTALGSRIRWITLRLGFLSSSVSTTAMVARTVFVALKSAFLQNSPSICSQGFAFSLTICIQVE +>Ac3315_3/4_0.828_2597 +NSDLDTMTALGSRIRWITRRFGFLSSSVSTTSIVARTVFVALKSALLQNSPNICSHGLAFSRTICMQVE +>PsIsotig06401_01089_2384 +NSDLDTITALGSRIRWITLRLGFLSSSVSTTSIVARTVFVALKSAFLQNSPNICSQGFAFSLTICMHVE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_46.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pp_882_1/1_1.000_2312 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLALLIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRRQLLIYENINKEMDKTLSEIKKLLEKQKVADEQEKLRRIQEERERERKKKEEEERKQREEEEQKKLKAEMET +>PsIsotig15436_07981_1677 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLAALIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRRQLLIYESINKEMDKTLAEIKKLLEKQKVAEEQERLRRIQEERERERKKKEEEERRKREEEEQKRLKAEMEA +>Pf127_1/1_1.000_1072 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLAALIKKVKIWLIKSRWRKAQWGVLSVIKLKNKIIYRRQLLIYEGINKEVDKTLVEIKKLLEKQKVAEEEERLRRIQEERERERKKKEEEERRKREEEEQKKLKAEMEA +>Ap1670_3/5_0.667_5194 +FKFGLTKVFFRPGKFAEFDKIMTSDPENLATLIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRKQLLIYEGINKEMDKTLAEIKKLLDKQKVAEEQERMRRIQEERERERKRKEEEERKKREEEERLRLKAEMEA +>Ac2574_1/1_1.000_4696 +FKFGLTKVFFRPGKFAEFDKIMTSDPENLATLIKKVKIWLIKSRWRKAQWGTLSVIKLKNKIFYRRQLLIYEGINKEMDKTLAEIKKLLDKQKVAEEQERMRRIQEERELERKRKEEEERKKQEEEERLRLKAEMEA +>Pg1Pg2_ContigI_2586 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLALLIKKVKLWLIKSRWRKAQWGALSVIKLKNKIIYRRQLLIYESVNKEMDKTLTDIRKLLEKQKVAEEQERMRRIQEERERERKRKEEEERQKREEEEQKRLKVEMEA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_47.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pg1Pg2_ContigII_47 +QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>Ac120_1/1_1.000_522 +QKDIKDGKYSQVLSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>Ap1431_4/4_0.500_851 +QKDIKDGKYSQVLSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHMKTTGRRGRTVGVSKKK +>Pp_11407_1/1_1.000_522 +QKDVKDGKYGQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>Pf74_1/1_1.000_506 +QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>PsContig17553_00005_681 +QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_50.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Ac2592_1/1_1.000_1693 +ERAMAPAGDGAFTIGKGVLAGASAVGLGMLCYYGLGMSNQVGAIDRAAIWPEEVRQRIKDTYMYFGGSLIFTAASAVAVSRSPVMMRLVMRNGWLTIIGTMAAMIGSGMVVRSLPYKKGFGAKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYALQPYDPINNSVGIYLDTINIFIRIATILAGG +>Pf687_1/1_1.000_1628 +ERAMAPAGDGAFTVGKGMLAGVSAVGLGMLCYYGLGMSNQVGAIDRAAIWPNIVRQRIKDTYMYFGGSLIFTAASAVAASRSPFMMRLVMRNGWLTIIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYAVQPYDPINNSVGIYLDTINIFIRIATILAGG +>PsContig29267_00170_1133 +ERAMAPAGDGAFTAGKGMLAGVSALGLGMLCYYGLGMSNQVGAIDRAAIWPNIVRQRVKDTYMYFGGSLIFTAASAVAASRSPVMMRLVMRNGWMTLIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMIHSGIVGAVIAPITLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYAVQPYDPINNSVGIYLDTINIFIRIATILAGG +>Pp_2968_1/1_1.000_1595 +ERAMAPAGDGAFSIGKGLVAGMSAVGLGMLCYYGLGMSNQVGAIDRAAIWPDIVRQRVKDTYMYFGGSLMFTAASAVAASRSPMVMNLVMRNGWLALIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMVHSGVVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAVCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGLYSVAMYGGLALFGAFLLYDTQKIIHRAENHPVYANQPYDPVNNSVGIYLDTINIFIRIAMIMGGG +>Ap2039_1/1_1.000_1819 +ERAMAPAGDGAFTIGKGVLAGASAVGLGMLCYYGLGMSNQVGAIDRAAIWPDVVRQRIRDTYMYFGGSLIFTAASAVAVSRSPVMMRLVMRNGWLTIIGTMAAMIGSGMVVRSLPYKEGFGSKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYALQPYDPVNNSVGIYLDTINIFIRIATILAGG +>Pg1Pg2_ContigI_3254 +ERAMAPAGDGAFTLGKGMLAGVSAVGLGMLCYYGLGMSNEVGAIDRAAIWPNVVRQRVKDTYMYFGGSLVFTAAAAVAASRSPMVMRLVMRNGWLALIGTMAAMIGSGMVVRALPYKEGFGSKQMAWIVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSIGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIHRAENHPVYAMQPYDPINNSVGIYLDTINIFIRIATILAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_53.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>PsIsotig04438_00541_1468 +SWLLGKWRSEDGQGIYPTIKDFKYIEELEFFQVGQPNIQFNFYAFNAETKKPMHREVGFIRVTPDLSKVALVSAQNTGLADIEEGTYNDKEKELRVESCALGRMSFGKLPETKIARIFR +>Ac19848_1/1_1.000_822 +SWLLGKWRSEEGAGHYPTIKDFKYIEEVEFFQVGQPNIQFSFYAFNAETKKPMHREVGFIRVKPDLSKVAFISAQNTGLAEVEEGTYNDKDKELRFESHTIGRLTFGKPPETKIARIFR +>Pf5916_1/1_1.000_798 +SWLLGKWRSEDGHGHYPTIKDFKYIEELEFFHVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFVSAQNTGLAEVEEGTYNDKEKELRFESHTVGRLTFGKPPETKIARIFR +>Pg1Pg2_ContigI_2557 +SWLLGKWRSEDGQGHYPTIKDFKYIEELEFIQVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFISAQNTGLAEVEEGTYNEKEKELRFESHTVGRLTFGKPPVTKIARIFR +>Ap4677_1/1_1.000_1142 +SWLLGKWRSEEGAGHYPTIKDFKYIEEVEFFQVGQPNIQFSFYAFNAETKKPMHREVGFIRVKPDLSKVAFISAQNTGLAEVEEGTYNDKDKELRFESHTIGRLTFGKPPETKITRIFR +>Pp_619_3/4_0.500_1588 +SWLLGKWRSEDGSGQYPTIKGFKYIEELEFFHVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFVSAQSTGLAEVEEGTYNDKEKELKFESHTVGRLTFGKPPVTKIARIFR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_57.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pp_4624_1/1_1.000_408 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHILYLGGVYRGGHDVLVRAKLALTDSGVTMQITVRSTDSSAAEVIASAVG +>Ap20_1/1_1.000_3490 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVYRGGHDVLVRAKLALTESGVTMQITVRSTDASAAEVIASAVG +>Pf2182_1/1_1.000_391 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRAKLALTDNGVTMQITVRSTDSSAAEVIARAVG +>Pg1Pg2_ContigI_4321 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRSKLALTENGVTMQITVRSTDSSAAEVIARAVG +>Ac769_1/1_1.000_3492 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVYRGGHDVLVRAKLALTESGVTMQITVRSTDASAAEVIASAVG +>PsIsotig22043_14588_2117 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRAKLALSENGVTMQITVRSTDASAAEVIARAVG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_58.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>Pf3163_1/1_1.000_300 +SSSDSDSHSRSSSSDSSSSSGSSSSGTSRSSSSSSSSSSKSRSRGRNRSVSRGR +>Ac5819_1/1_1.000_1087 +SSTDSDSHSRSSSSDSSSSSGSSSSGSSRSSSTSSSSSSKSRGRARNRSISRGR +>Pp_5864_1/2_1.000_1207 +SSSDSDSHSRSSSSDSSSSSGSSSSGSSRSSSSSSSTSSKSRNRGRNRSASRGR +>Pg1Pg2_ContigI_943 +SSSDSDSHTRSSSSDSSSSSGSSSSGSSRSSSSSSSTSSKSRSRGRNRSPSRGH +>Ap10018_1/1_1.000_1141 +SSSDSDSHSRSSSSDSSSSSGSSSSGSSRSSSTSSSSSSKSRGRARNRSISRGR +>PsIsotig05647_00837_2779 +SSSDSDSHSRSSSSDSSSSSGSSSSGTSRSSSSSSSSSSKSRSRGRNRSVSRGR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_60.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,12 @@ +>PsIsotig13857_06402_734 +ERFFGGGARRNDFSISDCLVTAENSSS +>Ap1982_1/2_1.000_2775 +ERFFGGGALRKDFSISDCLVTAENSSS +>Pp_26038_1/1_1.000_265 +ERFFGGGALRKDFSISDCLVTAENSSS +>Ac6601_1/2_1.000_1710 +ERFFGGGALRKDFSISDCLVTAENSSS +>Pg1Pg2_ContigI_6747 +DRFFGGGARRKDFNISDCLGTAENSSS +>Pf3398_1/1_1.000_178 +ERFFGGGARRNDFSISDCLVTAENSSS
--- a/test-data/sep_aa/orthogroup_1_sp6_sp6.fasta Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Pfi556Transcrip -VNKEPPTRRANAKLRVDQLKYDCQHLMREQEEREREALLSHHFEQNDSSTSVMIDAALQHNQRLSDAHRGMDDLLASG ->Ph45239g1i1 -VNKEPPTRRANAKLRVDQLKYDCQHLLREQEEREREALLSHHFEPNDSSTSVMIDAALQHNQRLTDAHHGMDDLLSSG ->Pg1Pg2ContigI38 -VNKEPPTRRANAKLRVDQLKYDCQHLMREQEEREREALLSHHFEPNDSSTSVMIDAALQHNQRLSDAHHGMDDLLSSG ->Ac100091/110006 -VNKEPPTRRANAKLRVDQLKYDCQHLMREQEEYEREALLSHHFEPNDSSTSIMIDAALQQNQRLSDAHHGIDDLLSSG ->Pun44302Transcr -VNKEPPTRRANAKLRVDQLKYDCQHLLREQEEREREALLSHHFEPNDSSTSVMIDVALQHNQRLGDAHHGMDELLAGG ->Pal7268Transcri -VNKEPPTRRANAKLRVDQLKYDCQHLMREQEEREREALLSHHFEPNDSSTSVMIDAALQHNQRLSDAHHGMDDLLSSG
--- a/test-data/sep_aa/orthogroup_1_sp8_sp8.fasta Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ ->PsContigII15300 ------------------------------------------------------------------------------ ->Pg1Pg2Pg2115381 -YSVLSTSSLHGENIMLTSEAVTADGGRSGPLFVVSQATLDQIKSEKNVVSEQTAMMDSALLESEDPSAPALVQYSES ->Pal3389Transcri -YSVLSTSSLHGENIMLTSEAVTADGGRSGPLFVVSQATLDQIKSEKNVVSEQTAMMDSTLLESEDPSAPALVQYSES ->Pun14364Transcr -YSVLSTSSLHGENIMLTSEAVTAEGGRSGPLFVVSQATLDQIKSEKNMVSEQTVMMNNTLLESEDPNAPTLVQYSES ->Ph35190g1i1 -YSVLSTNSLNGENIMLTSEAVTADGGRNGPLFVVSQATLDQIKSEENMVSEQNAMMGSSLLESEDPNAETLVQYPES ->Pp13976c0seq1 -YSVLSTSSLQGENIMLTSEAVTEDGSRNGPLFVVSQATLDQIKSELNIVSEQTVMMDSTLLESEEP------------ ->Ac100631/110004 ----------QGENIMLTSEAVTEDGSRNGPLFVENIMLTSEAVTGDGGRSGPLFVVSQATLDQIKSERNIVSEQPSM ->Pfi19278Transcr -YSVLSTSSLHGENIMLTSEAVTADGTRSGPLFVMSRAALDQIKSEKNIVSEQSAMMDSTLLESEDPNATTLVQYSES
--- a/test-data/sep_aa/orthogroup_2_sp6_sp6.fasta Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Pun7052Transcri -GEVIKGSVPLNSGTFDKLVPKFKAALVKFDEMYPYGDKHNEYKKLAEAAVSQPDLLVGEVNIAD ->Pal182Transcrip -GEVIKGSVPLNSGTFDKLVPKFKAALVKFDEMYPYGDKHKEFKKLAEAAISQPDLLVGEVNIAD ->Ap245451/110001 -GEVVKGSVPLNSGTFDKLVPKFKAALIKFDEMYPYGDKHNEYKKLAEAAIGQPDLLVGEVNIAD ->Ac100811/110008 -GEMVKGSVPLNSGTFDKLVPKFKAALIKFDEMYPYGDKHNEYKKLAEAATGQPDLLVGEVNIAD ->Pg1Pg2ContigI71 -GEVIKGSVPLNSGTFDKLVPKFKAALVKFDEMYPYGDKHKEFKKLAEAAISQPDLLVGEVNIAD ->Ph41010g1i3 -AEVVKGSVPLNSGTFDKLVPKFKAALVKFDEMYPYGDKHNEYKKLAEAAISQPDLLVAEVNIAD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_109_with_3_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,6 @@ +>Lf38763_1/1_1.000_387 +aaggccttgcgccggaacattgcggtgaactgctcgctgatgcgcttgaagagttcctggatggccgtgctgttgccgatgaaagtgccagacatcttgaggccgcgcggcgggatgtcgcagacagcggtcttgacgttgttcgggatccactcgacgaag +>Bj1919_1/1_1.000_456 +aaggccttacgacggaacatggcagtgaactgctcactgatgcgcttgaacagctcttggatggcggtgctgttgccgatgaaggtgcctgacatcttgaggccacgtggtgggatgtcacagacggctgtcttgacattgttgggaatccattcaacgaag +>Bs30874_1/1_1.000_304 +aaggccttgcggcggaacatggcagtgaattgctcagagatgcgcttgaagagctcttggatggcagtgctgttaccgacaaatgtaccggacatcttgaggccacgaggagggatgtcacaaacagcagtcttgacattgttggggatccattcgacgaag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_113_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bs16883_1/1_1.000_765 +caggagttcaaagaagccttcacaatgattgaccagaacagagacggcttcattgacgagagtgacctggcctccatgttccagcagaccggtcgcgaggctgagcccaaacagctgaaggagatgttggctgaggctcccggcacgctcaactttactaacttcctcacgctcttcggcgagaagctgcacggaactgaccccgagaggaccctgcttgatgccttcaagatgttcgacgttgaacgcaagggtatcctgtctgaagaatacctgaaggacctcctggtgaacgttggtgaccagttctccaaggatgagatcaaacaaacatgg +>Lf12022_1/1_1.000_613 +caggagttcaaggaggcgttcacgatgatcgaccagaaccgggacggcttcatcgacgagaacgacctggccgccatgttccagcagaccggacgcgaggctgagcccaagcaactgagagagatgttggccgaggcgccagggaccctcaacttcaccaacttcctcaccttgttcggcgaaaaacttcacgggactgacagcgagcgcaccctgacagacgccttcaagatgtttgacgaggccgggaaaggttacatttcagaggagtaccttaaggacctcctggttaacgttggtgaccagtactctaaggatgagattaaacagacgtgg +>Ha10806_1/1_1.000_456 +caggagttcaaggaagccttcaccatgatcgaccagaacagagatggcttcatcgatgagaacgacctggcttctatgttccaacagaccggtcgtgaggctgaacccaagcagctgaaggaaatgctggccgaggcgcccggcacgctcaacttcactaacttcctcaccttgttcggtgagaagttgcacggtactgacccggagaggacgctcctcgatgccttcaagatgttcgatccggaaggcaaaggggtcctggcggaagaatacttaaagactctcctggtggaagttggtgaccagttctccaaggacgagatcaaacagacgtgg +>Bj297_1/1_1.000_561 +caggagttcaaggaagccttcaccatgatcgacacgaaccgtgacggttttattgacgagtctgatctcgctgctatgtttcagcagaccggtaaggaagccgacccgaaaacgctgaaggagatgattgctgaggcacctggaaccttgaatttcaccaatttcctcacactctttggtgagaagcttcatggaaccgactctgagcgcaccctcattgacgccttcaagatgtttgacgatgagggcaagggtgtgctagcggaagattacctcaaggacctactggtggaggttggtgaccagtttaacaaggatgagcttaagcagacgtgg
--- a/test-data/sep_nuc/orthogroup_1_sp6_sp6.fasta Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Pfi556Transcrip -gttaacaaggaaccgccgacgaggagggcgaacgccaaattacgagttgatcagttaaaatacgattgccaacacttaatgagggagcaggaagaacgtgaaagggaggctttgctttcacatcattttgagcagaatgactcatcaacgtcagtgatgattgacgcagccttacagcacaatcagcgactgtcggatgcgcatcgtggaatggatgacttgttggctagcggc ->Ph45239g1i1 -gttaacaaggaaccgcccactaggagagcgaacgccaagctgagagtggatcagctgaagtatgattgtcaacatctactgagggaacaagaggaacgtgaaagggaagcattgctttctcatcattttgagcccaatgactcatctacatcagtcatgatcgatgcagctttacagcacaatcagcgattgacagatgcccatcatggcatggatgatctgttatctagtggt ->Pg1Pg2ContigI38 -gttaacaaagagccgcccacaagaagagccaatgccaagcttcgagttgaccagctaaaatacgactgtcagcatctaatgagggagcaggaagaacgtgagagagaagcactgctttcacaccattttgaaccaaatgattcatctacatcagtcatgattgatgcagctttacagcacaatcagcggctgtcggatgcacatcatggcatggacgatctgttatccagtggc ->Ac100091/110006 -gtcaacaaggagccgccgaccaggagagcaaatgcaaaacttcgagtggaccagctgaaatacgactgccagcatttaatgagagagcaagaagaatatgaaagggaagctttgctttcacatcactttgaaccaaatgattcgtccacatcaattatgattgatgcagctttacaacaaaaccagcgactgtcagatgcacatcatggcatagatgatttgctgtccagtggc ->Pun44302Transcr -gttaataaggagccgccgacaagaagggcaaatgccaagctgcgtgtagaccaactgaaatacgactgccagcatttactcagggagcaggaagaacgtgaacgagaggccttactttctcaccatttcgaaccaaatgattcatccacgtcagtcatgattgacgtagccctgcagcacaaccagcgattgggcgacgcacatcatggtatggatgagttgttggctggcggc ->Pal7268Transcri -gttaacaaagagccgcccacaagaagagcgaatgccaaacttcgagttgaccagctaaaatacgactgtcagcatcttatgagggagcaggaagaacgtgagagagaagcactgctttcacaccattttgaaccaaatgattcatctacatcagtcatgattgatgcagctttacagcacaatcagcggctctcggatgcacatcatggcatggacgatctgttatccagtggc
--- a/test-data/sep_nuc/orthogroup_1_sp8_sp8.fasta Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ ->PsContigII15300 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pg1Pg2Pg2115381 -tacagtgtgctgtcaaccagtagtctgcatggagagaatattatgcttacatcagaagcagttacagcagatgggggaagaagtggtccattatttgttgtgtcacaagccactttagatcagatcaagtcagagaagaatgtggtctcagagcagactgctatgatggacagcgccttgttggaatctgaagatccaagtgcaccagcacttgttcagtactcagaatct ->Pal3389Transcri -tacagtgtgctgtcaaccagtagtctgcatggagaaaatattatgcttacatcagaagcagttacagcagatgggggaagaagcggtccactgtttgttgtgtcacaagccactttagatcagatcaagtcagagaagaatgtggtctcagagcagactgctatgatggacagcaccttgttggaatctgaagatccaagtgcaccagcacttgttcagtattcagaatct ->Pun14364Transcr -tacagtgtgctctcaactagcagtctacatggtgaaaacattatgcttacatccgaggcagtaacagctgaaggaggcaggagtggtccactgtttgtcgtttcacaggcgactttagaccagataaaatcagagaagaacatggtctcagaacaaacagtcatgatgaacaatactttgctggagtcagaggatccaaatgcaccaacacttgttcagtattcagaatct ->Ph35190g1i1 -tatagtgtattgtcgacgaacagtttgaatggagaaaatataatgcttacatcggaagcagttactgctgatggtggaagaaacggtccattatttgttgtttcacaagccacactggaccagatcaagtcagaagagaatatggtgtcagaacagaatgctatgatgggtagtagtttactggaatctgaagatccaaatgcagagactcttgttcagtaccctgaatct ->Pp13976c0seq1 -tacagcgtactttcaacaagcagtttacagggtgaaaacattatgcttacatctgaggcagttactgaagatggaagccgaaatggtccattgtttgttgtttctcaagcaacattagaccagataaaatcagagctgaatatagtttcagaacagacagttatgatggacagtacattattggaatctgaagagcca--------------------------------- ->Ac100631/110004 ----------------------------------gaaaatataatgcttacctcggaagctgttacaggggatggaggcaggagtggcccactgtttgtcgtgtcacaagcaacattagaccagatcaaatcagaaaggaatattgtatcagaacagccatccatgatggacaatacgctgttggattctgaagatccaaatacagcagcacttgttcaatactcagaagct ->Pfi19278Transcr -tacagtgtactgtcaacaagcagcttgcatggagagaatattatgcttacatcagaagcagttacagcagatggcacaagaagtggacccttgtttgtcatgtctcgagctgcattagaccaaatcaagtctgagaagaacatagtgtcagagcagagtgctatgatggacagcacactgcttgaatctgaagatccaaatgcaacaacacttgtgcaatactcagagtct
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_253_with_2_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,4 @@ +>Ha10499_1/1_1.000_784 +ttctggatcagctgggatcgtggcctggtgcgagtcggggagggcacgcgccgcaaccaccagcccttcctcgtgtggaacgtccccgagaacaagcagcacggggtcaactgcatcgccgtctcctccgggcctgggtcggagggcgagtgggagttc +>Bj32890_1/1_1.000_2739 +ttctgggtgagctgggaccgcggctcggtgcgggttggcgaggggtcgcgccgcactcaccagcccttcctggtgtggaacgtgcccgagaacaagcagcacagcgtcaactgcatagcagtctcctccgggcccggctccgagggcgagtgggagttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_283_with_2_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,4 @@ +>Ha1337_1/1_1.000_1215 +gacttcttgatcttctcttcgaacagatcctttttgttgaggaaaagaatgatagaggtatcggtgaaccatttgttgttacagatcgagtcgaacagcttc +>Bs2095_1/1_1.000_1167 +gacttcttgatcttctcttcgaataaatccttcttattaaggaagagaataatagaggtgtccgtgaaccatttgttattacaaatagagtcgaacagcttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_299_with_2_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,4 @@ +>Bj17018_1/1_1.000_567 +tgcttcccgtccaaccaggaagttttctcggtacagatgaaaaactgtgatccgtttgtgttagggccagcgttcgccatcgacagcataccaggccctgtgtgcttcaaagtgaaattttcatcagcaaac +>Bs1426_1/1_1.000_513 +tgcttcccgtccagccagtcggtcttgacggtacagaggaagaactgcgacccgttggtgttggggccggcgttggccatggagaggataccgggtccagtgtgctttagggtgaagttctcgtcagcgaac
--- a/test-data/sep_nuc/orthogroup_2_sp6_sp6.fasta Tue Jul 03 10:55:46 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Pun7052Transcri -ggtgaagtcatcaagggatcggttcctctaaattctgggacttttgataagttggtacccaaattcaaagcagcattggtcaagtttgatgagatgtatccttatggtgacaaacacaatgagtacaagaagttagctgaggctgctgtatcacaaccagatctccttgttggagaggtcaacatagctgac ->Pal182Transcrip -ggtgaagtcatcaagggatcggttcctctaaattctgggacgtttgataagctggtgccaaagttcaaagcagcattggttaagtttgatgagatgtatccttatggcgacaaacacaaagagtttaagaagttagcagaagctgctatatcccagccagacctacttgttggagaagtaaacatagcagac ->Ap245451/110001 -ggcgaagtggtcaaaggatcggttcccttaaattctggcacttttgacaagctggtgccgaagttcaaagctgctctcatcaagtttgatgagatgtatccatatggagacaaacacaatgaatacaaaaagttagctgaagctgcgattggacaacctgacctccttgtgggcgaggtgaatatagcagac ->Ac100811/110008 -ggcgagatggtcaaaggatcggttcccttaaattctggcacctttgacaagctggtgccgaagttcaaagctgctctcatcaagtttgatgagatgtatccatatggagacaaacataatgaatacaagaagttagctgaagctgcgactggacaacctgacctgcttgtgggcgaagtgaatatagcagac ->Pg1Pg2ContigI71 -ggtgaagtcatcaagggatcggttcctctaaattctgggacgtttgataagctggtgccgaagttcaaagcagcattggttaagtttgatgagatgtatccttatggtgacaaacacaaagaatttaagaagttagcagaagctgctatatcccagccagacctacttgttggagaagtgaacatagcagac ->Ph41010g1i3 -gccgaagtcgtcaagggatccgtccccctaaattcggggacatttgacaagctggtgccaaagttcaaggcagcactggttaagtttgatgagatgtatccatatggagataaacataatgaatacaagaagctagcagaggctgctatatcacagccagacttgctagttgcagaggtaaacatagcagac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_301_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Ha10118_1/1_1.000_897 +gaggatgatgaggaacaggtagacgatgtccaagtagagctgcagcgctccgaacacgtggtcctccggggacagctcgaacttcttgcctccgatcagcatctgtgtgtcgtaagccaggaacatggagaa +>Lf311_1/1_1.000_384 +gaggatgatgagaaagaggtagatgatgtcgaggtagagctgaagtgctccgaacacgtggtcctctggcgacagtcggtacttcttgttgcccatcagcatctgggtgtcatacgccaggaacatagagaa +>Bs27070_1/1_1.000_699 +gaggatgatgatgaagaggtagacgatgtccaggtacagctggagcgcaccgaacacgtgatcctccggggagagctcatgcttcttaccgccaaccagcatctgggtgtcgtacgccaggaacatagagaa +>Bj17798_1/1_1.000_1215 +gaggaagatgaggaagaggtagactatgtccaggtacagctggagcgcaccgaacacatggtcctctggggagagctcatacttcttaccgccaatcagcatctgggtgtcatatgcgaggaacatagagaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_316_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bs27803_1/1_1.000_1664 +gtgaacgcgccccctgtcccctcctctcgcgacactgcgctcaccatcgccgcagacaagggccactaccgctttgtggaactgctcctctccagaagcgctgccgtagacgtgaagaacaagaaggggaactctcctctgtggttggcttgcaacggtgggcacctggatgtggtgcagttactcgtgaacgccaaggcggatatcgacagccaggacaaccgcaaggtgtcgtgcctcatcgcggccttccgcaaaggtcacgtgaaggttatcaaatggatggtgaagcatgtggcacagttcccttcggaccaggagtgcatgcgatacatctcaaccatcacggataaggagctgctgaaaaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaggcagcggaggcgaaccggcacgcctctatcctcctggaacagttggaccgcgagaagagcctggaggagagcaagaaggcggccgcagcccgcaagcgcgagaagcgacgccggaagaagaaggagaagcaggagcaggcgaacaacaaaaaccaggcacacaagcgaagtcggaacactgaggtgagctcgaacagcagcagtagcagcgagtcgaatggcaagacgaagagcaagaagagcaagaaggccgagcgc +>Bj26780_1/1_1.000_2698 +gtgaatgcgccccccgttccctcctctcgcgacactgcgctcaccattgccgcagacaagggccactatcgctttgtggagctgctcctctcgagaagtgcggccgtagacgtaaagaacaaaaaggggaactctcctctatggttggcttgcaacggtgggcacttggacgtcgtgcagttattagtgaacgccaaggctgacattgacagtcaggacaaccgcaaggtatcatgcctcattgcggctttccgcaaaggtcacgtcaaggtgatcaaatggatggtgaagcacgtggcacagttcccttcagaccaggagtgcatgcgatacatctcaaccattacggacaaggagctgctgaaaaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaggcagcggaggctaaccgccacgcttccattctcctggagcagctggaccgtgagaagagcttagaggagagcaagaaggcagcggccgcccgcaagagggagaaacgacgccgcaagaagaaggagaagcaggaacaggcgaacaacaaaaaccaggcgcacaagcggagtcgtaacaccgaggtgagctcgaacagcagcagtagcagcgaatcaaatggcaagacgaagagtaagaagagcaagaaggctgagcgc +>Ha1883_1/1_1.000_5577 +gtgaacgcgccacccgtgccctcttcacgtgacaccgccctcaccatcgccgcagacaagggccactaccgcttcgtcgagctgctcctctcccgcagtgctgccgttgatgttaagaacaagaagggcaactcgccgctctggttagcctgcaacgggggtcacctggatgtggtgcagctgttggtgaatgctaaggcagacatcgacagtcaggacaaccgtaaggtgtcgtgcctcatcgccgccttccgtaaggggcatgtcaaggtcatcaagtggatggtgaagcatgtggcccagttcccgtcagaccccgagtgcatgcgctacatctcgaccatcactgacaaggagctgctgaagaaatgccaccagtgcatggagattatcgtcagtgccaaggaccggcaagcagccgaggccaaccgccacgcatctatcctactagagcagctcgaccgagagaagagcctagaggagagcaagaaagccgccgcagcccgcaagagggagaagcggcggcgaaagaagaaggagaaacaggagcaggcaaataacaaaaaccaagcccacaagcggagtcgcaatttggaagtgagcagcaatagtagcagtagcagcgagtccaacggcaagaccaagagcaagaagagcaaaaaggccgagcgg +>Lf1892_1/1_1.000_9654 +gtgaacgcgccgcctgtgccgtcatcccgcgacaccgcgctcaccatcgccgctgacaaggggcactaccgctttgtggagctgcttctctccaggagtgctgctgtggatgtaaagaacaagaagggaaactctcctctctggctggcctgtaatggtgggcacctggacgtggtgcaattattggtgaacgccaaggcggacatcgacagccaggacaaccgcaaggtgtcgtgtctgattgcagctttccgcaaaggtcatgtgaaggtcatcaagtggatggtgaagcatgtggcccagttcccgtcggaccaggagtgcatgcgctacatctcgaccatcacagataaggagctgcttaagaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaagcagcagaggcgaaccggcatgcgtcaattctcctggagcagctcgaccgcgagaagagtctggaggagagtaagaaggccgcagccgcccgcaagcgggagaaacgtcggcggaagaagaaggagaagcaggaacaggcaaacaacaaaaaccaggcccacaaacgaagtcgtaacactgaggtgagctccaacagtagcagcagcagcgagtcaaacggcaagaccaagagcaagaaaagcaagaaggcggagcgg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_335_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Lf1038_1/1_1.000_963 +gcgccgcatggcgacggtcgagtagttgcagtgcgcgccagcgccgttccagtctcccggcatcggcttcgggtcgaagctgacgacgatcccgaagtcctcagcgacacggtgcaggacgtagcgcgccatccacaggtcgtcgcccatctggatgccctcacacggacccacctggaactcccactgtcccggcatcacctcggcgttcgtgccggcgatcttgatgtcggcgta +>Bs16552_1/1_1.000_1152 +ctccctcatggccagcgtcgagaagttggtgtgtgccccggcaccgttccagtctccgggcattggcttggggtcgaaactgacgacgatgccaaagtcttcggcgactctgtgcaggatgaatctggccatccagaggtggtcgcccatgctgattccctcacagggtcccacttggaactcccactgggcaggcatcacctcagcgttggtaccggcgatcttgacgccggcgta +>Bj389_1/1_1.000_1311 +ttctctcatggcttgtgtggagtagttggtgtgtgcacctgcgccgttccagtctccgggcatgggtttggggtcaaaggtgacgatgactccgaagtcctctgcgactctatgcagcaagtagcgggccatccagaggtggtctcccatctcaatgcccaggcacgggccaacctggaactcccactggccgggcatgacctcggcgttggttccggctattttgactcctgcgta +>Ha2081_1/1_1.000_1176 +ctccctcatggccttggtggagtagtttgtgtgtgcaccggcaccattccagtctccgggcatgggtttggggtcgaaggtgacgatgacaccgaagtcctctgctacacggtgcagcaggtagcgggacatccacaggtggtcgcccatgtcgatacccaggcacggccctacctggaactcccactgggcaggcatgacctcagcattagtaccagagatgttgacccctgcgtg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_343_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Ha10325_1/1_1.000_531 +ccccgtactgggtgccccacgctgaccgcatccactacatctctaaggactgtgagagggactggttcaacgactgggagtgtatggagtgctgcaacggagatctctgcaactactatgtca +>Bs3268_1/1_1.000_471 +ccccctactgggtgccccacgctgaccgcatctactacatctccaagaactgcgagcgcgactggttcaacgactgggagtgcatggagtgttgcaacggcgacctgtgcaactactacgtca +>Lf56088_1/1_1.000_447 +ccccttactgggtgccctacggagaccgcgcctacttcgtctccaagaactgcgagcgcgactggttcgacgactggggctgtgtggagtgctgctcgggcgacctgtgcaactactacgtca +>Bj5017_1/1_1.000_456 +ccccctactgggtgccccatgctgaccgcatctactacatctccaagaactgcgagcgggactggttcaacgactgggagtgcatggagtgttgtaacggcgacctgtgtaactactacgtca
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_368_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Lf51152_1/1_1.000_999 +aggcggatggtgtttgagaagaacatgatgttcatccgagaccacaacatggaggctgaccttggacacaagtccttccgggttggggtcaagaaccaggcacaatgtggatcctgctgggcgttctccgccattggggccctggaaggtcaacacttcaggaagacaggggatctcgtctctctatctgagcagaacctggtcgactgctcaacaacagaagga +>Ha12847_1/1_1.000_855 +aggcggatgatcttcgagaagaacatgaacttcatccgtgaacacaacatggcagctgatcttggccacaagaccttccgtgtcggtgtcaagaaccagatgcaatgtggatcatgctgggccttctccgctactggctcccttgaaggtcaacatttcaagaagacaggaaagctggtctccctttcagaacagaatcttgttgactgttcccaagctgaagga +>Bs1045_1/1_1.000_633 +aggcgaatggtgttcgagaagaacatgatgttcatccgggaccacaacatggaagctgaccttgggcacaaatccttccgggtcggagtcaagaaccaggaacaatgtggttcctgctgggccttctctgcaactggctcactggaggggcagcacttcaagaagacaggcaagcttgtctccctgtcagagcagaacctggttgactgctcccaggccgaagga +>Bj108003_1/1_1.000_523 +aggcgaatggtgtttgagaagaacatgatgttcatccaggaccacaacatggaggctgacctggggcacaagtccttccgggttggaatcaagaaccagggggcttgtggctcctgctgggctttctctgcaactgggtcgctcgagggacagcacttcaagaagactggtaaccttgtctccctgtcagaacagaacctggttgactgttctaaggctgaagga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_404_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Lf14756_1/1_1.000_456 +gtcagcctttccatcacggttgctgtcaagtttgtcggcgagtccgtctttgttctggtc +>Ha5212_1/1_1.000_491 +gtcctccttgccatcacggttgctgtccagcttgtcagctactccatcgttgttctggtc +>Bj16996_1/1_1.000_378 +gtccttcttgccatcacggttgctgtcaaatttgtctgcgagcccatcgttgttttggtc +>Bs10543_1/1_1.000_387 +gtccttcttgccatcgcggttgctgtcaagcttgtcagcgagcccatcgttgttctggtc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_442_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj29526_1/1_1.000_478 +acacacaatgaaggagttggcatctccagcatagtagaagccataattatagccagaagcgcagtcaccctcaaaatgtccgaggtagtaaaactggccagctccaacatgaactgggtaggctcccaaagtgcggtagttgaactcattgttgaaaccaaatccttctccatatccata +>Bs16935_1/1_1.000_456 +acatacgatgaaggagttggcatctccagcatagtagaatccatagttgtagccagaggcgcaatcaccattgaaatgtccaaggtagtagaactggccagctccaacatgaactgggtaggctccaaaggtacgatagttgaactcattgttgtagccaaatcctactccatatccata +>Ha22482_1/1_1.000_398 +acacacaatgaaggagtcagcatttccagcaaagtagaagccataattgtatccaccagcacagttaccattgaactgcccaaggtagtagaactggccatttcctacatgaactgggtaggcaccaaatcctcggtagttgtactcattgttgaagccataccctactccagcaccaga +>Lf10136_1/1_1.000_570 +gcacacgatgaaggagttagcatcctcagtgtagtagaagccgtaattgtagccattggcgcagttaccattgaagtttccaaggaaatagaactgcccagctgcaatattgaaaggatatgctccgaatccatgatagttgaactcattgttatagccatatcctactccatatccata
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_487_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj104219_1/1_1.000_544 +ggcttctgggacaagttgatccttgagccttacggccggcagcgggacatagtctac +>Lf26378_1/1_1.000_6633 +ggcttctgggacaagctgatactggaaccatacggccggcagcgagacattgtctac +>Ha278_1/1_1.000_2763 +ggcttctgggacaagttgatcctggagccgtacgggcggcagcgtgacgtggcctac +>Bs54896_1/1_1.000_618 +ggtttctgggacaagctgatccttgagccttatgggcggcagcgggacatcgtctac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_508_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj115168_1/1_1.000_390 +tcctcctcctcctccgagctgctgacgtcaccaaatatgtcttcctccaggaatttgctaatgttctccgatgcggctgcgttctcgaccttcttggcctccgatgagttcagtggattgaacacgtccccg +>Lf36714_1/1_1.000_1599 +tcctcctcttcctcggagctgctcacgtcgccgaagatatcctcctccaggaatttgctgatgttctccgaggcggctgcgttctccaccttcttagcttcggaggaattcagcgggttgaaaacatcgccg +>Bs6083_1/1_1.000_337 +tcctcttcctcctcagagctgctcacatcaccaaagatatcctcctccaggaatttgctgatgttctccgacgcggctgcgttctcgaccttcttggcttcagatgagttgagcgggttgaacacatccccg +>Ha18272_1/1_1.000_681 +tcctcctcctcttctgagctgctcacgtcgccgaagatatcctcctctaagaatttgcttatgttttcagaggcggcagcattttccactttcttggcctctgatgagttaagtgggttgaagacgtctccg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_544_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj19203_1/1_1.000_2676 +gaactgaagcgagcagacttcaagctgatcggcaagggcaagtctgacccctactgcaagatctacatcgggtcccagatgtacaagacacgagtgatcgaaaacaccattaacccagtctggaacagctacttcgaggcggttgttgaccaaaaacatggccaatttgcggagcttgaggtacttgaccaggatcctggggaggatgacgaactgggaacggcaagtattgatattgagaacgtggcagtaaagggctcattggacacgtggctccctcttgagaatgtcgagaccggcatggtgcacatccgggcaatatggcttcacctcagcaagaaccctaaagacctg +>Lf110082_1/1_1.000_1416 +gaactgaagagagccgacttcaaactggtcggcaagggcaagtccgacccctactgcaagatctacatcggtgctcagatgtacaagacgaaggtaattgagaacacgatcaacccggtctggaacagctacttcgaggcggttgttgaccagaagcacggtcaatttgcggagctcgaggtacttgacaaagatccgggtgatgatgacgagttgggcacagcgagtatcgacatcgagaatgttggcgacaagggcacattggacacgtggctgccgctggagaacgtggagacgggtatggtacacatccgtgccatatggctgcacctgagtaaggacccggccgacctg +>Ha37107_1/1_1.000_642 +gaactgaagcgggccgacttcaaactggtggggaaaggcaaatcggacccctactgcaaaatatacattggcgcacagagcttcaagaccaaagtgatagaaaacactatcaatcctgtatggaacagctactttgaggcggtagtggaccagaagcatggacaattcgctgaactggaagtgctcgatcaggatcctggagaagatgacgaacttggaacggcgagtgtggacatccagaatgtaggtgaacatggctcaattgacacgtggctccccctggagaatgtggacactggcatggtgcacatccgtgctatgtggctgcacctgagtaaggaccccgctgatctg +>Bs13030_1/1_1.000_2652 +gaactgaaacgggcagacttcaaactggtcgggaagggcaagtcggacccctactgcaagatctacatcggcgcccagatgtacaagacgaaagtcatcgaaaacaccattaacccagtctggaacagctacttcgaggcggttgttgaccaaaaacatggtcaatttgcggagcttgaggtacttgaccaggatcccggtgaagatgacgaactgggcacagcaagtattgacattgaggacgtgggtgcaaaaggctcactggacacgtggcttcccctggagaacatcgaaactggcatggtgcacgtccgggccatctggctccacctcagcaaggacccgaacgacctg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_546_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Ha41649_1/1_1.000_527 +ctcaccccggtacctgtagacgaacccgctcacacctgtacactacattcacgctacacctgcctcattaag +>Lf11086_1/1_1.000_2517 +ctcaccccagtacctgtggacgagccggcacacacgtgcaccctccatgcacgctacacgtgtctcgtgaag +>Bs41282_1/1_1.000_485 +ctgagcccggtgcctgaagacgagccagcacacacatgcactctgcatgcacgctacacgtgcctggtgaag +>Bj19624_1/1_1.000_1584 +ctgagcccggtgcctgtagacgagcctgcccacacgtgcacccttcatgcacgctacacgtgtctggtgaag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_588_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj3220_1/1_1.000_3147 +agtttggagaccgagtgcccgccgacgtgcgcgttagctcatggatttaaggtggacaactcctcgctgactggggaatctgagcctcagactagaaccgcagagttcacgaatgataacccgctcgagaccaagaacctcgccttcttctcaacaaatgctgttgaaggcacgtgtcgcgggattgtagtgagcactggggaccgcaccgttatgggccggatcgccaacctggcatccggactcgagatgggccagactccgatcgcacgtgagatcgaacatttcatccacatcattactggtgtcgctgtattcctcggcgtagccttctttatcgtcgctttcatccttggttactactggcttgatgctgtcatcttcctcatcggtatcattgtcgccaatgtgcccgaaggtctgctggctaccgtcacggtgtgcctgactctgaccgctaagcgcatggcgtccaagaactgtctcgttaagaacctggaggccgtggaaacacttggctccacatccacaatctgctccgataaaacgggaactctcactcagaaccgtatgactgtcgctcacatgtggttcgacaaccgcatcattgaggcggacaccactgaggatcagtcagcagatgcgggctgtgacgcggcatctgccacttggcaaagtttggcgcgtattgccatgttatgtaaccgcgctgagttcaagatgggacaggagaaccttcctgtactaaaaagggaatgtaacggcgacgcctccgagtctgcgctgctgaagtgcgcagagctatctatcggcaaggtgagagagttccgcgcaaagcacaagaaagcagttgaaattccattcaactcaaccaataaatatcaggtctctgtgcatgagatgccggacgatccgcgctacctgcttgtaatgaagggcgcccctgagcgcatcctggaccgctgcactaccatcctcattaatggcgaagagaaacccgtgtctcccgagtggaaggaggccttcgaacattcctacatggagttgggaggccttggagagcgcgtactcggattctgtgactacatccttgatgttgcaaaattcccacgtggctatccgtttgactcggaggaagagaacttccccctgaccggcctgcgcttcgttggtcttatgtccatgatcgaccctccacgagccgccgtgccggatgccgtgggcaaatgtcgcagtgctgggattaaggtgatcatggtgacgggcgaccatcccatcaccgccaaggccatcgcgaagggcgttggcatcatctctgagggaaatgaaactgtagaggacatcgctgcacggctcaacatacccgtcagtgaagtcaaccccagggacgctatggcatgtgttgtacacggctctgacctgcgtgatatgacccctgctcaaatagacgacatcctcagcaaccacacggagattgtattggcacgtacttcaccgcaacagaaactcatcattgtcgagggctgccaacgtcaaggcgccattgttgctgtcacaggcgatggggttaacgactcccctgccctaaagaaagccgatatcggagttgccatgggcattgctggcagcgacgtgtcgaaacaagcggctgacatgattcttctcgacgacaacttcgcatctattgtaactggtgtagaagagggccgtctgatcttcgacaacctcaagaagtcgatcgcctacaccctcacctcgaacatccccgaaatctctcccttccttctcttcatcctggccgatgtgccactgcccctgggaaccatcaccatcctgtgcattgatctcgggaccgaccttgtcccagcgatctccttggcctacgagcaggctgaaagtgacatcatgaaacgccagccccgtgatcctctccacgacaagctcgtgaacaacaggctgatcggcatggcctacgggcaggtcggtatgatccaggcatcggccgggttcttcgtctacttcgtcatcctcgccgagaatggcttcttgccatcacggcttctcggcatccgggaaagttgggactcgaaggctatcaacgacgagctcttatggtcaggagtggacatacgcccagcg +>Bs118_1/1_1.000_3114 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+>Ha3202_1/1_1.000_3108 +agttcggggacagggttccggctgacgtgcgtgtcagcacacggtttcaaggtcgacaactcctccctgactggtgaatccgagccgcagacaagaactgctgagttcaccaacgaaaaccctctagaaaccaagaacctggcattcttctcaaccaatgccgtcgaaggtacctgccgtggtgttgtcatcagcaccggtgacagtaccgtcatgggccgtattgccaacctggcctccggtctcgagatgggccagactccgattgcccgcgagatcgagcatttcatccacatcattactggggtagccgtcttcctgggcatatcattctttgtcatcgccttcatcctcggctattactggctcgatgccgtcatcttccttatcggtatcatcgtcgccaacgtgcccgaaggtctgctcgccaccgtcacggtgtgcctgaccctgactgccaagcgtatggcgtccaagaactgtctggtgaagaacctggaagccgtggagaccctcggctccacctccaccatctgctccgacaagaccggcacactcacccagaaccgtatgaccgtcgcccacatgtggttcgacaaccgcatcgtcgaggctgacaccactgaggaccagtcagcagacgcatgctacgactcctcctccccgacttggttggccctggcctgcatcgctatgctctgtaaccgtgctgagttcaagatgggccaagaatctgtacctgtactaaagagggaatgtaacggtgatgcctcggagtccgctctgctgaagtgcgttgagctgtccatcgggaaggtggtcgagttccgtgccaggcacaagaaggccgtagaaattccattcaactcaaccaacaaataccaggtgtctgtacacgaggtaccagatgatcctcgctacctgctggtgatgaagggagcccccgagcgtatcctggaccgctgctccactatcctgatcaacggcgaggagaagcccctctcggatgagtggagggaggccttcaaccaggcctacctcgagttgggaggcctcggagagcgtgtgcttggattctgtgactactaccttgacgccgctcagtacccccatggctaccccttcgactctgaggaagaaaacttccctctaactggactccgcttcgtcgggcttatgtccatgattgaccccccacgtgctgctgtgcctgatgctgtcggcaaatgccgcagcgcaggcatcaaagttatcatggttaccggcgaccaccccatcactgccaaggctatcgccaaaggtgtcggaattatctccgagggcaacgagaccgtggaagacatcgctgccaggcttaacattcccgtcagcgaagtcaacccaagggatgcgaaggcttgcgttgttcacgggtccgacctacgcgatatgaccccggctcagattgatgatatcctcgccaaccacaccgaaatcgtgtttgcacgtacctcaccccagcagaaactcatcattgtagaaggttgccagcgccaaggagccattgtggctgtcactggtgacggtgtgaacgactcaccggccctcaagaaggctgacatcggtgttgccatgggcatcgctggtagcgacgtgtccaaacaggccgccgacatgattctgctggatgacaacttcgcctctattgttacaggcgtggaggaggggcgtctgatctttgacaacctgaagaaatcgatcgcctacactctgacctcgaacatcccagagatctcccccttcctcctcttcatcctggctgacgtcccacttcctctcggaactatcaccatcctgtgtattgatctcgggaccgaccttgtccctgctatctcccttgcctacgagcaggcggagagcgatattatgaagcgccagccccgtgatcctcttcacgacaagctcgtgaaccacaggctgatcggcatggcttatggccaaattggcatgattcaggccactgccggcttcttcgtttacttcgtcatcttggccgagaatggcttctggccatcccgtcttctcggcatccggatgcgttgggattcgaaagcggtgaacgacgagctcctatggacaggagtggacctacgcccagcg +>Lf11686_1/1_1.000_3102 +agttcggggaccgcgtcccggccgacgtcagggtcagcccacggctttaaggttgacaactcatcactgaccggagaatctgaacctcagtcaagaactgccgagtttaccaacgagaatccactcgagaccaagaaccttgctttcttctccacgaatgctgttgaaggtacgtgccgtggcgtcgtggtcggcacgggggaccgcaccgttatggggcggattgcaaacctggcgtctggcctcgaagttggtcagactccaatcgcacgagagatcgagcatttcatccacatcatcacgggcgtggccgtgttcctcggtgtcgccttcttcatcgtcgccttcatccttggctactactggctcgatgcagtcatcttcctcattggtatcattgtcgctaatgtccccgaaggtctgcttgctactgtcacagtatgcctgacactgaccgccaagcgcatggcgtccaagaactgtctcgttaagaaccttgaggctgtcgagacgctcggatctacctccaccatctgctccgacaagactggcaccctcacccagaaccgcatgacggtcgcccacatgtggttcgacaaccacatcgtggaagccgacacgaccgaagaccagtccacggaggccgggtgcgactctgcatcccccacatggcagtgtctgatccgcgttgctatgttatgtaaccgtgccgagttcaaaatgggacaagataaattccctgtactgaaaagggaatgtaatggcgatgcttctgaatctgccttgttgaagtgtgccgaactctccattggcaaagtaattgagttccgtgccaaacacaagaaagccattgaaattcccttcaactcaaccaacaaatatcaggtgtctatacatgagctgccagatgacccacgctacctgctcgtaatgaagggcgcccctgagcgcatcctggaccgttgtgccaccatcctcataaatggggaggagaagccgatgagtgaggaatggaaagaggcatttgagcagtcctacatggagctgggcgggctcggcgagcgcgtgctcggattctgcgacttcattctggatgctgaaaagtttccccggggctatccattcgatgctgacgaggagaacttcccactgacagggctgcgctttgtggggctcatgtcgatgatcgaccccccgcgtgctgctgtcccagacgcggtcggcaaatgccgcagcgctggaatcaaagtcatcatggtaactggggaccacccgatcactgccaaggccatcgctaagggtgttggcattatctctgagggcaatgaaactgtagaggatatcgccgcacggctcaacatacccctcagccaggtcaagcccagtgatgcgaaagcttgtgtcattcatggctctgacctccgtgatatgacacctgctgaaatagatgacatgctccgaaaccacactgaaatagtgatggcgcggacctcgccccagcagaaactcatcattgtggagggctgccagcggcagggcgccattgtagctgtcacgggtgacggtgtgaatgattcacccgccctaaagaaagcagatattggagttgccatgggcatcgctggtagcgacgtgtcaaaacaagcggccgacatgatccttcttgatgacaactttgcatctattgtcactggcgtagaagagggacgtctgatcttcgacaacctgaagaaatcgattgcttacactcttacttcaaacatcccggaaatttccccattccttctgttcatcctggctgatgtgccactgcctctgggaaccatcaccatcctgtgtattgatcttgggacggatctcatccccgccatctcactcgcatacgagcaggctgaaagcgacatcatgaagcgccagccccgtgaccctctccacgacaagctcgtcaacaaccggctcatcggcatggcctatgggcagattggcatgattcaggcctctgccggcttctttgtttactttgtgattcttgcagagaatggctttttaccgtgggatctgtttggcatccgtcaaaactgggattccagggctgtaaacgataagctcctatggacaggagtggacgtacgcccagcg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_623_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj55915_1/1_1.000_1497 +ctggtgcgtctgtcccagcaggagctgatcgactgctcgtggggagaggggaacaatggatgtgatggcggagacgacttcctcgcctaccagtggatttccaaacacggactggcc +>Lf5592_1/1_1.000_1659 +ctggtacggctgtctcagcaggagctaatcgactgttcgtggggagaggggaacaacgggtgtgacgggggtgatgacttccgcgcctacaagtggattactaagcacggactggcc +>Ha1592_1/1_1.000_1710 +ctggtgcgcctgtcccagcaggagctggtagactgttcgtggggtatgggtaacaacgggtgtgatggcggagaggacttccgtgcttaccagtggatcaccaagcacgggctggcc +>Bs34509_1/1_1.000_1086 +ctggtgcgcctgtcacagcaggagctgatcgactgctcgtggggagaagggaacaatgggtgtgacggaggagaggactttcgtgcctaccagtggatcagcaagcacgggctcagc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_651_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bs8968_1/1_1.000_1776 +tgtgaagaggatgcaggaggtctgctgcagactgaatgcctgtcctcctggaagcaggacaacacgacgctggttctcgtccgccgattagacgtcagcaag +>Ha12591_1/1_1.000_492 +tgtgaggaggatgttggaggtctgatgcaaactgaatgtctatcatcgtggaaacaggataacacgacactggtgctggtgcgccgtctcgactcccacaaa +>Lf56294_1/1_1.000_1773 +tgtgagcaggatgctggtggtttactgcagactgagtgcctctccacgtggaaacaggacaacaccacactggttcttgtcaggcgcctagacgtcagcaag +>Bj88046_1/1_1.000_797 +tgtgaggaggatgcgggtggtttgctgcagacagaatgtctctcctcctggaagcaggagaacacgacgctggtgctcgtccgccgtctggacgtcagcaaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_660_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bj102_1/1_1.000_1566 +gcagatggtatcgtgaagacgatgcgctccaaggcaggccccagctccaaggaacttaaggccgccgacgaggtcgagaagtttatcaatggaaaagatcttgtcatcgttggcttcttcgagtctgatggcagt +>Lf3141_1/1_1.000_1467 +tcagatgggattgtaaagacgatgcgctccaaggcgggacccacatcgatggaattaaaggctgttgacgatgttgagaaatttattggcggaaaaggtcacgtcgttgttggtttcttcaagtcggaaggcagt +>Bs17280_1/1_1.000_360 +gcagatggtattgttaagaccatgcgtggcaaggctggcccaagctccaaggaactcaagtctggtgacgaagttgagaagtacatctcaggaaacgacattgtcttcgttggtttcttcgaggctgagggcagt +>Ha1450_1/1_1.000_1497 +gcagatggtattgttaagaccatgcgtggcaaggctggcccaagctccaaggaactcaagtctggtgacgaagttgagaagtacatctcaggaaacgacattgtcttcgttggtttcttcgaggctgagggcagt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_696_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Lf46816_1/1_1.000_3195 +aagctcaacgcgcagctcctaaaccacccgctcacccaccagcacttcgtccccgcactcatgaagttctacgtcgacattgagacgactggtgcgagtagcgaattctatgacaagttcacggtgcgctaccacacgtccattatcctgaagacgctgtgggaaatccctatgcaccaagcgcgcattgtggaggaggccaccggggcagtttgtccgtttcac +>Bj11264_1/1_1.000_1503 +aagctcaactcacagctcctcaaccacccactgacgcatgagcatttcgtaccagcactcatgaagttctatgtcgacattgagacgacgggtgcaagtagtgagttttacgacaagttcacagtacggtaccacacgtccatcatcctgaagaatatgtgggacatccccatgcaccaggcacgcattgtgaaggaagcgactggggcagtttgtgcgatttac +>Ha2853_1/1_1.000_2274 +aaactcaacactcagctactcaaccacccgctaacacatcaacactttgtacccgcactcatgaagttctacgtagacatagagacgacgggggcgagcagcgagttctatgacaagttcacggtacgctaccacatcagtatcatcctcaagaccatgtgggacatccccatccaccagggccgcatcgtacaagaagccatcgggccagtttgtgcgtttcac +>Bs8429_1/1_1.000_306 +aagctcaactcgcagctcctcaaccacccgctcacacatgagcatttcgtaccggcactcatgaagttctacgtcgacattgagacgacgggggctagtagtgagttctacgacaagttcactgtgcgatatcacacgtccatcatcctgaagaatatgtgggacatccccatgcaccaagcacgcattgtgaaggaggcaactggagcagtttgtgcggtttac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_707_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Ha58565_1/1_1.000_582 +tgtgtaagatctcagactttggcagctcacgggacatcgcacagagccggcagtacgagagccgcacacagaaccggttaccgatacgttggatggcgcctgagtctctgtatgattgcatgtacagtatcaagtctgacgtctggtcctttggggttctactctgggagatcgtcacac +>Lf5218_1/1_1.000_3096 +tgtgtaagatctcggactttggcagcgcgcgggacatcgcgcagagccggcagtatgagagccgcacacagaaccgcctgcccatccggtggatggcgcccgagtcgctgtacgactgtatgtacagcgtcaagtccgacgtgtggtccttcggcgtgctgctgtgggaaattgtcacac +>Bj116010_1/1_1.000_312 +tctgcaagatctctgactttgggagttctcgcgacatcgcacagagccggcagtatgagagtcgaacgcagaaccgccttccaatccggtggatggcgcctgagtcgctgtacgactgcatgtacagcgtcaagtcggacgtctggtccttcggggttctactctgggaggtcgtcacgc +>Bs1374_1/1_1.000_1335 +tgtgcaagatctccgactttggaagttctcgcgacatcgcacagagccgacagtatgaaagccggacgcagaaccgccttccaatccggtggatggcgcctgagtcactgtatgactgcatgtacagcatcaagtcagacgtctggtcctacggcgttctgctgtgggagatcgtcacgc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_727_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Lf1012_1/1_1.000_735 +tatggctgggtctaccgaaatgggcgggacttgtccggcttcatcgacggaactgagaatccggctgacgggagctacgtgattacccaacgatgggttcataacctggcgaagataaagaagacaaaagat +>Ha1000_1/1_1.000_1200 +tacggctgggtgtaccagaatggtcgtgacttgtcagggttcattgatggtactgagaaccctgccgacggaagttacgtgatcacacaacgatgggttcacaacttggagaagatcaagaagactaaagat +>Bs2375_1/1_1.000_555 +tacggctgggtgttccgccaggggcgcgacctgtccggcttcatcgacggcaccgagaacccggcggacggaagttacgtgatcacccagcggtgggtccatgaccttgaaaagattaaaatgacaaaagtg +>Bj12534_1/1_1.000_1269 +tacggctgggtgttccgccagggacgcgacttgtccggcttcatcgacggcaccgagaacccggccgacggaagttacgtgatcacccagcgatgggttcataaccttcccaagatcaagaagaccaaagat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_761_with_4_species.fasta Mon Sep 24 04:34:39 2018 -0400 @@ -0,0 +1,8 @@ +>Bs10197_1/1_1.000_1857 +cagatcggcttcacgaccgacccccgctcgtctcggtcgtcgccttactgcacggacgtggcgcgcgttgtcaacgcgcccatcttccacgtcaacgccgacgaccccgaggccgtgatgcacgtgtgcaaggtggctgccgagtaccgctccgagtggggcaaggacgtcgtcatcgacttggtctgttaccggcgtaatggtcacaacgagatagatgagcccatgttcacccagccgctcatgtacaagcgcatccatcagcagccatccatcctcaaactctactccgccaagctcatcgacgagaaagttgtttcgcaggatgagtatgagctcgaggtggcaaagtacgacaaaatctgcgaagacgcctatgtgaacgccaagaaggagacggtcacccgcaatagcctgtggctcgactcgccctggcccggcttcttcgacagt +>Ha1458_1/1_1.000_3087 +cagattggcttcacgacagacccccgctcatcgcgctcgtcaccctactgcacggacgtggcacgtgtcgtcaatgcacctattttccacgtaaatgccgatgaccccgaggctgtcatgcacgtatgcaaggtggcagccgagtaccgtgctgagtggggcaaagatgtggtcattgacttggtgtgctaccggaagaacggccacaatgagactgacgagcccatgttcacccaaccgctcatgtacaaacgtatccaccagcagccgtccatccttaaacagtactctacgaagctcatcaccgagggcatcgtcagccaggaagagtatgaggttgaagttgcaaagtatgacaagatttgtgaggatgcctaccttaacgcaaagaaggagacggtcacacgtaacagtcagtggctagactctccatggccaggcttctttgatcgt +>Bj16755_1/1_1.000_2085 +cagattggcttcacgactgaccctcggtcatcacggtcgtcaccgtattgcacagacgtggcacgcgtcgtgaacgcgcccatcttccacgtgaacgcggatgaccccgaagccgtcatgcatgtgtgtaaggtggctgccgagtaccgcgcagaatggggcaaggacgtcgtcattgacttggtatgctaccggcgcaatggtcacaacgagatagatgagcctatgtttacgcagccactcatgtacaagcgcatccaccagcagccgtccatccttaagctctactctgccaagctcattgatgagaaaatagtttcacaagatgaatatgaggttgaagtggcaaagtacgataaaatctgtgaagatgcttacataaatgccaagaaggagactgtcacccgcaacagtctatggctcgactcgccttggccaggattctttgactgt +>Lf14456_1/1_1.000_2623 +cagatcggcttcacgacagacccacggtcctcccgctcgtccccatactgcacggacgtggcacgtgtcgtgaacgcacctatcttccacgtgaacgcggacgaccccgaggccgtgatgcacgtgtgtaaggtggccgccgagtaccgcgccgagtggggcaaggacgtcgtcatcgacttggtgtgttatcgccgtaacggtcacaacgagatcgacgagccgatgttcacacaaccgctcatgtacaagcgtatccaccaacagccgtccatcctcaaactgtactcggcaaaactcatcgacgagaagatcgtctcacaggaggaatacgagcttgaagtggccaagtacgacaagatctgcgaggacgcgtacctgaacgccaagaaggagacagtgacccgaaacagcctatggctcgactcaccctggcccggcttcttcgatcgt