Mercurial > repos > abims-sbr > cds_search
changeset 9:640ef4c06ed5 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit f1ba8d136e0129f3e8435b25a95f70f697d51464-dirty
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--- a/CDS_search.xml Mon Mar 12 06:30:49 2018 -0400 +++ b/CDS_search.xml Tue Jul 03 10:54:18 2018 -0400 @@ -12,20 +12,18 @@ <expand macro="python_required" /> </requirements> - <command><![CDATA[ - #set $infiles = "" + <command><![CDATA[ #for $input in $inputs ln -s '$input' '$input.element_identifier'; - #set $infiles = $infiles + $input.element_identifier + "," + echo '$input.element_identifier' >> list_files; #end for - #set $infiles = $infiles[:-1] ln -s $__tool_directory__/scripts/dico.py . && python $__tool_directory__/scripts/S01_find_orf_on_multiple_alignment.py - $infiles $__tool_directory__/scripts/code_universel_modified.txt $length.min_length_seq + list_files > '$log' && python $__tool_directory__/scripts/S02_remove_too_short_bit_or_whole_sequence.py @@ -137,66 +135,47 @@ <param name="out_CDS_filter" value="both" /> <output_collection name="output_BESTORF_aa" type="list"> <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_1_with_3_species.fasta" /> - <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_2_with_2_species.fasta" /> - <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_3_with_3_species.fasta" /> <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_14_with_2_species.fasta" /> </output_collection> <output_collection name="output_BESTORF_nuc" type="list"> <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_1_with_3_species.fasta" /> - <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_2_with_2_species.fasta" /> - <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_3_with_3_species.fasta" /> <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_14_with_2_species.fasta" /> </output_collection> <output_collection name="output_CDS_aa" type="list"> <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_1_with_3_species.fasta" /> - <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_2_with_2_species.fasta" /> - <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_3_with_3_species.fasta" /> <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_14_with_2_species.fasta" /> </output_collection> <output_collection name="output_CDS_nuc" type="list"> <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_1_with_3_species.fasta" /> - <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_2_with_2_species.fasta" /> - <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_3_with_3_species.fasta" /> <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_14_with_2_species.fasta" /> + </output_collection> + + <output_collection name="output_filter_aa" type="list"> + <element name="orthogroup_1_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_1_with_2_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_14_with_2_species.fasta" /> + </output_collection> + <output_collection name="output_filter_nuc" type="list"> + <element name="orthogroup_1_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_1_with_2_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_14_with_2_species.fasta" /> </output_collection> <output_collection name="output_filter_aa" type="list" count="4"/> <output_collection name="output_filter_nuc" type="list" count="4"/> </test> + <test> <param name="inputs" ftype="fasta" value="inputs/orthogroup_1_with_4_sequences.fasta,inputs/orthogroup_6_with_4_sequences.fasta,inputs/orthogroup_7_with_3_sequences.fasta,inputs/orthogroup_8_with_4_sequences.fasta,inputs/orthogroup_12_with_5_sequences.fasta,inputs/orthogroup_14_with_4_sequences.fasta" /> - <param name="nb_species_keep" value="2" /> - <param name="methionine" value="yes" /> - <section name="length"> - <param name="min_length_seq" value="50" /> - <param name="min_length_subseq" value="15" /> - <param name="min_length_nuc" value="50" /> - </section> - <param name="out_BESTORF" value="both" /> - <param name="out_CDS" value="both" /> - <param name="out_CDS_filter" value="both" /> - <output_collection name="output_BESTORF_aa" type="list"> - <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_1_with_3_species.fasta" /> - <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_2_with_2_species.fasta" /> - <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_3_with_3_species.fasta" /> - <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta" /> - </output_collection> - <output_collection name="output_BESTORF_nuc" type="list"> - <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_1_with_3_species.fasta" /> - <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_2_with_2_species.fasta" /> - <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_3_with_3_species.fasta" /> - <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta" /> - </output_collection> - <output_collection name="output_CDS_M_aa" type="list"> - <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_06_CDS_with_M_aa/test1/orthogroup_6_with_2_species.fasta" /> - </output_collection> - <output_collection name="output_CDS_M_nuc" type="list"> - <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_06_CDS_with_M_nuc/test1/orthogroup_6_with_2_species.fasta" /> - </output_collection> - </test> - - <!-- tests with name "locus_x_spy.fasta" --> - <test> - <param name="inputs" ftype="fasta" value="inputs/locus1_sp5.fasta,inputs/locus1_sp7.fasta,inputs/locus2_sp4.fasta,inputs/locus2_sp6.fasta" /> <param name="nb_species_keep" value="2" /> <param name="methionine" value="no" /> <section name="length"> @@ -206,57 +185,26 @@ </section> <param name="out_BESTORF" value="both" /> <param name="out_CDS" value="both" /> - <param name="out_CDS_filter" value="both" /> + <param name="out_CDS_filter" value="both" /> <output_collection name="output_BESTORF_aa" type="list"> - <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_2_with_7_species.fasta" /> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_4_with_6_species.fasta" /> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_14_with_2_species.fasta" /> </output_collection> <output_collection name="output_BESTORF_nuc" type="list"> - <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_2_with_7_species.fasta" /> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> - <output_collection name="output_CDS_aa" type="list"> - <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_05_CDS_aa/test2/orthogroup_2_with_7_species.fasta" /> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_05_CDS_aa/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> - <output_collection name="output_CDS_nuc" type="list"> - <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_2_with_7_species.fasta" /> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_6_with_2_species.fasta" /> + <element name="orthogroup_7_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_7_with_3_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_14_with_2_species.fasta" /> + </output_collection> <output_collection name="output_filter_aa" type="list"> - <element name="orthogroup_1_with_4_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test2/orthogroup_1_with_4_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_14_with_2_species.fasta" /> </output_collection> <output_collection name="output_filter_nuc" type="list"> - <element name="orthogroup_1_with_4_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test2/orthogroup_1_with_4_species.fasta" /> + <element name="orthogroup_14_with_2_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_14_with_2_species.fasta" /> </output_collection> - </test> - <test> - <param name="inputs" ftype="fasta" value="inputs/locus1_sp5.fasta,inputs/locus1_sp7.fasta,inputs/locus2_sp4.fasta,inputs/locus2_sp6.fasta" /> - <param name="nb_species_keep" value="2" /> - <param name="methionine" value="yes" /> - <section name="length"> - <param name="min_length_seq" value="50" /> - <param name="min_length_subseq" value="15" /> - <param name="min_length_nuc" value="50" /> - </section> - <param name="out_BESTORF" value="both" /> - <param name="out_CDS" value="both" /> - <param name="out_CDS_filter" value="both" /> - <output_collection name="output_BESTORF_aa" type="list"> - <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_2_with_7_species.fasta" /> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> - <output_collection name="output_BESTORF_nuc" type="list"> - <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_2_with_7_species.fasta" /> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> - <output_collection name="output_CDS_M_aa" type="list"> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_06_CDS_with_M_aa/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> - <output_collection name="output_CDS_M_nuc" type="list"> - <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_06_CDS_with_M_nuc/test2/orthogroup_4_with_6_species.fasta" /> - </output_collection> - </test> + </test> </tests> <help>
--- a/scripts/S01_find_orf_on_multiple_alignment.py Mon Mar 12 06:30:49 2018 -0400 +++ b/scripts/S01_find_orf_on_multiple_alignment.py Tue Jul 03 10:54:18 2018 -0400 @@ -302,8 +302,8 @@ ############################################################ def ReverseComplement2(seq): # too lazy to construct the dictionary manually, use a dict comprehension - seq1 = 'ATCG-TAGC-atcg-tagc-' - seq_dict = { seq1[i]:seq1[i+5] for i in range(20) if i < 5 or 10<=i<15 } + seq1 = 'ATCGN-TAGCN-atcgn-tagcn-' + seq_dict = { seq1[i]:seq1[i+6] for i in range(24) if i < 6 or 12<=i<16 } return "".join([seq_dict[base] for base in reversed(seq)]) ############################ @@ -314,14 +314,16 @@ import string, os, time, re, zipfile, sys from dico import dico -infiles = sys.argv[1] -MINIMAL_CDS_LENGTH = int(sys.argv[3]) ## in aa number - -## INPUT / OUTPUT -list_file = str.split(infiles,",") +MINIMAL_CDS_LENGTH = int(sys.argv[2]) ## in aa number ### Get Universal Code -bash_codeUniversel = code_universel(sys.argv[2]) ### DEF2 ### +bash_codeUniversel = code_universel(sys.argv[1]) ### DEF2 ### + +## INPUT from file containing list of species +list_files = [] +with open(sys.argv[3], 'r') as f: + for line in f.readlines(): + list_files.append(line.strip('\n')) os.mkdir("04_BEST_ORF_nuc") Path_OUT1 = "04_BEST_ORF_nuc" @@ -350,16 +352,18 @@ name_elems = ["orthogroup", "0", "with", "0", "species.fasta"] # by fixing the counter here, there will be some "holes" in the outputs directories (missing numbers), but the groups between directories will correspond -n0 = 0 -for file in list_file: - n0 += 1 +#n0 = 0 + +for file in list_files: + #n0 += 1 count_file_processed = count_file_processed + 1 + nb_gp = file.split('_')[1] # Keep trace of the orthogroup number fasta_file_path = "./%s" %file bash_fasta = dico(fasta_file_path) ### DEF 1 ### BESTORF_nuc, BESTORF_nuc_CODING, BESTORF_nuc_CDS_with_M, BESTORF_aa, BESTORF_aa_CODING, BESTORF_aa_CDS_with_M = find_good_ORF_criteria_3(bash_fasta, bash_codeUniversel) ### DEF 4 - PART 2 - ### - name_elems[1] = str(n0) + name_elems[1] = nb_gp ## a ## OUTPUT BESTORF_nuc if BESTORF_nuc != {}: @@ -431,7 +435,7 @@ OUT6.write("%s\n" %seq) OUT6.close() - os.system("rm -rf %s" %file) + #os.system("rm -rf %s" %file) ## Print print "*************** CDS detection ***************"
--- a/scripts/S02_remove_too_short_bit_or_whole_sequence.py Mon Mar 12 06:30:49 2018 -0400 +++ b/scripts/S02_remove_too_short_bit_or_whole_sequence.py Tue Jul 03 10:54:18 2018 -0400 @@ -146,7 +146,8 @@ # 4.6 ## Correct the nb of sequence in the output name, if necessary n0 += 1 - name_elems[1] = str(n0) + name_elems[1] = file.split('_')[1] + #name_elems[1] = str(n0) name_elems[3] = str(len(new_bash_nuc.keys())) new_name = "_".join(name_elems) dico_dico[new_name] = [new_bash_aa, new_bash_nuc]
--- a/scripts/S03_remove_site_with_not_enough_species_represented.py Mon Mar 12 06:30:49 2018 -0400 +++ b/scripts/S03_remove_site_with_not_enough_species_represented.py Tue Jul 03 10:54:18 2018 -0400 @@ -157,7 +157,8 @@ ## 4.3 ## Change file name for output, depending the number of species remaining in the alignment n0+=1 - name_elems[1] = str(n0) + #name_elems[1] = str(n0) + name_elems[1] = file.split('_')[1] name_elems[3] = str(len(filtered_bash_aa.keys())) new_name = "_".join(name_elems)
--- a/test-data/inputs/locus1_sp5.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ ->Ac45601/110 ------------------------------------------------------------------------------------------------------------------------- ->Am32051/110 ------------------------------------------------------------------------------------------------------------------------- ->Ap54541/110 ------------------------------------------------------------------------------------------------------------------------- ->Pf28561/110 -agtgacggtgacgtcatcatcttggtgatcgtcacgctgagctacgtggatcaggcgtcgaacttctacgtcacttccgttctgccgcacggcttgacgaacgtactcttcgtcgctcta ->Ph75241/110 -------------------------------------ctgagctatctggatctggcttggaacttctacgt-------------------------------------------------
--- a/test-data/inputs/locus1_sp7.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am31481/110 -caaaacccgacaaaaatcaaaatgattcctccaaacgcatctctggtgaaatatgacaatcctgttcttgttagcaggaatacagacaagaaaacaccaagggcgcgtgctctcaaggtggctacacgtctagacgtagtcaatctacaggaggaactggatagacgtctacagcagagacaggcccgggaaacaggaatctgtccggtcagacgagagctctattcgcaatgctttgacgagttgattcgccaagtgaccattaactgtgctgagcgaggtttgttgttactacgtgttcgtgatgagatccgtatgacgatcgctgcctaccagaccctgtatgagagctctgtagcttttggtatgaggaaagccttacaagcagaacaaggcaaggccgacatggagagaaagatc ->Ap26441/110 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pf20921/110 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctacagcaaagactcgcccgagaaaccggcatctgttcaataagaagagaactctattcacagtgctttgatgaactgatccgtcaggtgacaatcaactgcgctgagcgagg-----------------------------------------------------------tgtatgagagcagcgtcgcttttggaatgaggaaagc------------------------------------------- ->Pu7631/1100 ----------------------atgattcctccgaaatcctctctggttaaatatgataatcc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te17661/110 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Th39471/110 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
--- a/test-data/inputs/locus2_sp4.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->Ac38641/110 -------------------------------------------tatgagaacatccgtaagagtcggcttgatgaccacatcagtgcccattctggcataaagaatcatgtgtgtgcagtgtgtgggaaggcctttgccgggcggaagcacatgcagagacatgaaaaaacacacctggaagtgaagccccttaagtgtgaacaatgtgaatatgccacaacacgaagagacaagttacgtgatcacattagaaagcatcacaaagccatggccatcagcttgggtatccttgatccaaa- ->Am55481/110 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Ap59291/110 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pg58451/110 -cataatggcaagaaattccggtgtacttttcctggctgtgcatatgagaacatacggaagagtcgtctcgatgatcacatcagtgctcacactggaattaagaatcatgtgtgctccatatgtggaaaggcatttgcaggacgcaaacatatgcagagacatgaaaagacacatttggaaattaagccgttaaagtgtgagcactgtgaatacgcaactacgcgcagagataaattacgtgatcacataagaaaacatcacagaaatattgccatcagcatgggtattcttgacccaaat
--- a/test-data/inputs/locus2_sp6.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Ac28061/110 -aaacacgctgctttagtcactgctctctacatttactgtctgggtacctttgaatgtggtgacaggtacataggacaccaaggtgtaaagcttgtgaggcgagtcctcatcctcattcctcttacgagccaatcgaactcgtactctgaatggaacatttctaattcccttggaccaaatgtgtttgttcagtcttgtctctatgcgtacatcttcagttcccatctgcttgtaggcaaattgtctgatagcctttatagcccgtggcgccctcttcttgaaccctattccatggattcgcttgtggatgttgatggtgtattcccgtgtcaccacctcgttggtgacagacttcttcttgcctttctcgcggcgtgtcatcgcttccgg ->Am30661/110 -----------ctttattcactgctctccacattcacggtctgg---------------------------------------------------------------------------------------------------------------------------cccttggaccagacgtgcttgttgagtcgggtctcgattcggacatcctctgtgcccatctgcttgaaggcaaactctcggatggctttcaccgcgcgaggcgccctcctcttgaagccaatgccatgtatacgcttgtggatgttgatggtgtattctcgggtcacgacctcctgggtcacggacttctt--------------------------------- ->Pg28571/110 ----------------gtcactactctccacatttactgtctgtgtacctttgaatgttgtaacaggtacataggagaccaaggtgtaaagtttgtgtggcgagtcttcatcttcattccttttacgagccaatcttacacgcacacggaatgggacatttctaattccctttgaccaaatgtgtttgttgagtctcgtctctatacgcacatcctcagtgcccatctgtttaaaggcaaactgcctgatagccttgatcgcacgaggtgccctcttcttgaaacctattccatgaattcttttgtggatattcactgtgtattctctagttaccacctcattggtaacagacttcttcttgcccttctcccggcgtgccatggcttc--- ->Ph73091/110 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aggcaaactgtctgatggctttgatggcacgtggcgccctcttcttgaacccaattccgtgaattcgtttatggatgtttatggtgtattcccttgttaccacttcattggtaacggacttcttctttcccttctcacggcgtg------------- ->Te26821/110 --------------------------------------------------------------------acataggtcactaatgtataaagtttgtgcggtgaatcttcatcctcatt--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Th44731/110 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cccatctgcttgttggcaaa------------------------------------------------------------------------------------------------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +RVAAMDTCQTRIRLSVYPANSVWPSADHARDIHWGGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFQTLTSLSQPQDTMMGF*VFGEKRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTIWRLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDITTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKIISGNCGVVAI*VTHPPCPWRVPRSVICSVMFL +>Ap1491_1/1_1.000_963 +RVAAIDTCHTRIRLSVYPANSVWPSADQARDIH*GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFHTLTSLSQPQDTMMGFWVFGENRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTI*RLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDMTTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKMISGNCGVVAIWVTHPPCPWRVPRSVICSVMFL
--- a/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap5072_1/1_1.000_437 -PNRCHCSRS*HFAAS*RRSGIRCS*SVRCGPCRFRGRSERARLD*GRCSSPGRWR*SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV*IGP*AVCP*PCSPWPSGPFSAP*RS ->Ac1013_1/1_1.000_525 -PSRCRCSQS*HFAAS*RRSRIRRS*SVRCGPCRWRGRS*RARLDQGRCSSLGKWR*PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV*IEP*VVCP*PCSLWP*GLFSAP*RS
--- a/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->Am3527_1/1_1.000_270 -????????????????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT????????????????????? ->Ap5050_1/1_1.000_243 -LLQKLVAD*EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF*PSPS ->Ac2173_1/1_1.000_330 -LLQKLVAD*EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF*PSPS
--- a/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -1,4 +1,4 @@ ->Ac6688_1/1_1.000_963 -RVAAMDTCQTRIRLSVYPANSVWPSADHARDIHWGGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFQTLTSLSQPQDTMMGF*VFGEKRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTIWRLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDITTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKIISGNCGVVAI*VTHPPCPWRVPRSVICSVMFL ->Ap1491_1/1_1.000_963 -RVAAIDTCHTRIRLSVYPANSVWPSADQARDIH*GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFHTLTSLSQPQDTMMGFWVFGENRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTI*RLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDMTTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKMISGNCGVVAIWVTHPPCPWRVPRSVICSVMFL +>Ap5072_1/1_1.000_437 +PNRCHCSRS*HFAAS*RRSGIRCS*SVRCGPCRFRGRSERARLD*GRCSSPGRWR*SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV*IGP*AVCP*PCSPWPSGPFSAP*RS +>Ac1013_1/1_1.000_525 +PSRCRCSQS*HFAAS*RRSRIRRS*SVRCGPCRWRGRS*RARLDQGRCSSLGKWR*PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV*IEP*VVCP*PCSLWP*GLFSAP*RS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +????????????????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT????????????????????? +>Ap5050_1/1_1.000_243 +LLQKLVAD*EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF*PSPS +>Ac2173_1/1_1.000_330 +LLQKLVAD*EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF*PSPS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +RVAAMDTCQTRIRLSVYPANSVWPSADHARDIHWGGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFQTLTSLSQPQDTMMGF*VFGEKRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTIWRLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDITTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKIISGNCGVVAI*VTHPPCPWRVPRSVICSVMFL +>Ap1491_1/1_1.000_963 +RVAAIDTCHTRIRLSVYPANSVWPSADQARDIH*GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFHTLTSLSQPQDTMMGFWVFGENRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTI*RLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDMTTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKMISGNCGVVAIWVTHPPCPWRVPRSVICSVMFL
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_1_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +?????????????????????????????????????????????????????????????VFLVVFH*LYQTLK*CGTN +>Ap2303_1/1_1.000_424 +???????????????FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN*LNKALKGCCAN +>Ac3644_1/1_1.000_1626 +QFIFTLFLVVIQSPHFNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN*LNKAFK*CCAN
--- a/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Te17661/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Ap26441/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Th39471/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Pf20921/110 -??????????????LSSFQKRRCSHT????????????????????LAQRS*LSPDGSVHQSTVNRVLFLLNRCRFLGRVFAV???????????????????????????????????????????????????????? ->Pu7631/1100 -???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????DYHI*PERISEES??????? ->Am31481/110 -SFSPCRPCLVLLVRLSSYQKLQSSHTGSGRQRSSYGSHHEHVVTTNLAQHS*WSLGESTRQSIANRALV*PDRFLFPGPVSAVDVYPVPPVD*LRLDV*PP*EHAPLVFSCLYSC*QEQDCHISPEMRLEESF*FLSGF
--- a/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -??????????????????????????????????????????????????FANKQM?????????????????????????????????????????????????????????????????????????? ->Te26821/110 -???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY??????????????????????? ->Ph73091/110 -?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA?????????????????????????????????????????????????????????????????????????????? ->Am30661/110 -???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE*???? ->Ac28061/110 -PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD*SSVF ->Pg28571/110 -?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD?????
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +PNRCHCSRS*HFAAS*RRSGIRCS*SVRCGPCRFRGRSERARLD*GRCSSPGRWR*SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV*IGP*AVCP*PCSPWPSGPFSAP*RS +>Ac1013_1/1_1.000_525 +PSRCRCSQS*HFAAS*RRSRIRRS*SVRCGPCRWRGRS*RARLDQGRCSSLGKWR*PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV*IEP*VVCP*PCSLWP*GLFSAP*RS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +????????????????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT????????????????????? +>Ap5050_1/1_1.000_243 +LLQKLVAD*EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF*PSPS +>Ac2173_1/1_1.000_330 +LLQKLVAD*EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF*PSPS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +cgggtagctgccatggacacctgccagacacggatcaggttgtctgtgtatcctgcaaacagcgtctggccatcagctgaccatgccagggatatacactggggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcaggtaacctgagtgtccaaagtggtttgtttttagtttgcagtttgtcagattccaaaccttaaccagtttgtcccagccacaagacacaatgatgggattctgagtgtttggtgagaagcgaacacatgatacccactctgtgtgtccatcttcctgaatggtgtacttgcatacaccgagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctggcggttatcagctgagaaggccacgcttagcacatcttttgtgtgtccgacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagagcgaactgtccatctgatgacataacaacgtcagacacgaaatgtccatgtccacgcaaggccttgcgagggaaaccgtagcgcgattcctcacgagtcagctgccacaggatgagcgatttgtctcttgaagccgacaaaataatatcgggaaattgtggcgttgtagcaatttgagttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt +>Ap1491_1/1_1.000_963 +cgggtagctgccatagatacctgccacacacgaatcaggttgtctgtgtatccagcaaacagtgtctggccatcagctgaccaagccagggatatacactgaggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcagataacctgagtgtccgaagtggtttgtttttagcttgcagtttgtcagattccacaccttaaccagtttgtcccagccacaggacacaatgatgggattctgggtgtttggtgagaatcgaacacatgatacccactctgtgtgcccatcttcctgaatggtatacttgcacaccccaagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctgacggttatcagctgagaaagccacacttagcacgtccttcgtgtgtccaacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagggcgaactgtccatctgatgacatgacgacgtcagacacgaagtgtccatgtccgcgcaaggccttgcgagggaagccgtaacgcgattcctcgcgagtcagctgccacagaatgagcgatttgtctctagaagccgacaaaatgatatcaggaaattgtggcgttgtagcaatttgggttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt
--- a/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap5072_1/1_1.000_437 -cccaatcgctgtcactgctctcgaagttgacattttgctgcttcatgaagaaggtcaggaattcgttgtagttgatccgtccgctgtggtccttgtcgatttcgtggacgatctgaaagagctcgtctggattgaggaaggtgttcatctcccggaagatggcgttgatctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtttgaattgggccttgagctgtttgcccttgaccttgtagcccttggccttcagggcctttttcagctccttgaaggtca ->Ac1013_1/1_1.000_525 -cccagtcgctgtcgctgctctcaaagttgacattttgctgcttcatgaagaaggtcaagaattcgtcgtagttgatccgtccgctgtggtccttgtcgatggcgtggacgatcttgaagagctcgtctggatcaaggaaggtgttcatctcttggaaaatggcgttaacctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtttgaattgagccttgagttgtttgcccttgaccttgtagcctttggccttgagggcttttttcagctccttgaaggtca
--- a/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->Am3527_1/1_1.000_270 -----------------------------------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag------------------------------------------------------------- ->Ap5050_1/1_1.000_243 -ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttctgaccttccccaagc ->Ac2173_1/1_1.000_330 -ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttctgaccttctccaagc
--- a/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -1,4 +1,4 @@ ->Ac6688_1/1_1.000_963 -cgggtagctgccatggacacctgccagacacggatcaggttgtctgtgtatcctgcaaacagcgtctggccatcagctgaccatgccagggatatacactggggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcaggtaacctgagtgtccaaagtggtttgtttttagtttgcagtttgtcagattccaaaccttaaccagtttgtcccagccacaagacacaatgatgggattctgagtgtttggtgagaagcgaacacatgatacccactctgtgtgtccatcttcctgaatggtgtacttgcatacaccgagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctggcggttatcagctgagaaggccacgcttagcacatcttttgtgtgtccgacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagagcgaactgtccatctgatgacataacaacgtcagacacgaaatgtccatgtccacgcaaggccttgcgagggaaaccgtagcgcgattcctcacgagtcagctgccacaggatgagcgatttgtctcttgaagccgacaaaataatatcgggaaattgtggcgttgtagcaatttgagttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt ->Ap1491_1/1_1.000_963 -cgggtagctgccatagatacctgccacacacgaatcaggttgtctgtgtatccagcaaacagtgtctggccatcagctgaccaagccagggatatacactgaggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcagataacctgagtgtccgaagtggtttgtttttagcttgcagtttgtcagattccacaccttaaccagtttgtcccagccacaggacacaatgatgggattctgggtgtttggtgagaatcgaacacatgatacccactctgtgtgcccatcttcctgaatggtatacttgcacaccccaagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctgacggttatcagctgagaaagccacacttagcacgtccttcgtgtgtccaacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagggcgaactgtccatctgatgacatgacgacgtcagacacgaagtgtccatgtccgcgcaaggccttgcgagggaagccgtaacgcgattcctcgcgagtcagctgccacagaatgagcgatttgtctctagaagccgacaaaatgatatcaggaaattgtggcgttgtagcaatttgggttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt +>Ap5072_1/1_1.000_437 +cccaatcgctgtcactgctctcgaagttgacattttgctgcttcatgaagaaggtcaggaattcgttgtagttgatccgtccgctgtggtccttgtcgatttcgtggacgatctgaaagagctcgtctggattgaggaaggtgttcatctcccggaagatggcgttgatctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtttgaattgggccttgagctgtttgcccttgaccttgtagcccttggccttcagggcctttttcagctccttgaaggtca +>Ac1013_1/1_1.000_525 +cccagtcgctgtcgctgctctcaaagttgacattttgctgcttcatgaagaaggtcaagaattcgtcgtagttgatccgtccgctgtggtccttgtcgatggcgtggacgatcttgaagagctcgtctggatcaaggaaggtgttcatctcttggaaaatggcgttaacctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtttgaattgagccttgagttgtttgcccttgaccttgtagcctttggccttgagggcttttttcagctccttgaaggtca
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +----------------------------------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag------------------------------------------------------------- +>Ap5050_1/1_1.000_243 +ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttctgaccttccccaagc +>Ac2173_1/1_1.000_330 +ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttctgaccttctccaagc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +cgggtagctgccatggacacctgccagacacggatcaggttgtctgtgtatcctgcaaacagcgtctggccatcagctgaccatgccagggatatacactggggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcaggtaacctgagtgtccaaagtggtttgtttttagtttgcagtttgtcagattccaaaccttaaccagtttgtcccagccacaagacacaatgatgggattctgagtgtttggtgagaagcgaacacatgatacccactctgtgtgtccatcttcctgaatggtgtacttgcatacaccgagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctggcggttatcagctgagaaggccacgcttagcacatcttttgtgtgtccgacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagagcgaactgtccatctgatgacataacaacgtcagacacgaaatgtccatgtccacgcaaggccttgcgagggaaaccgtagcgcgattcctcacgagtcagctgccacaggatgagcgatttgtctcttgaagccgacaaaataatatcgggaaattgtggcgttgtagcaatttgagttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt +>Ap1491_1/1_1.000_963 +cgggtagctgccatagatacctgccacacacgaatcaggttgtctgtgtatccagcaaacagtgtctggccatcagctgaccaagccagggatatacactgaggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcagataacctgagtgtccgaagtggtttgtttttagcttgcagtttgtcagattccacaccttaaccagtttgtcccagccacaggacacaatgatgggattctgggtgtttggtgagaatcgaacacatgatacccactctgtgtgcccatcttcctgaatggtatacttgcacaccccaagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctgacggttatcagctgagaaagccacacttagcacgtccttcgtgtgtccaacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagggcgaactgtccatctgatgacatgacgacgtcagacacgaagtgtccatgtccgcgcaaggccttgcgagggaagccgtaacgcgattcctcgcgagtcagctgccacagaatgagcgatttgtctctagaagccgacaaaatgatatcaggaaattgtggcgttgtagcaatttgggttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_1_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gggtttttcttgtagtattccactagctctaccagactctcaaatgatgcggtaccaat +>Ap2303_1/1_1.000_424 +--------------------------------------------ctttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaactaactcaacaaggctctcaaaggatgctgtgccaat +>Ac3644_1/1_1.000_1626 +cagttcatcttcacgttgtttcttgtagtcatacaaagccctcactttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaactaactcaacaaggctttcaaatgatgctgtgccaat
--- a/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te17661/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Ap26441/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Th39471/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pf20921/110 ------------------------------------------gctttcctcattccaaaagcgacgctgctctcataca-----------------------------------------------------------cctcgctcagcgcagttgattgtcacctgacggatcagttcatcaaagcactgtgaatagagttctcttcttattgaacagatgccggtttctcgggcgagtctttgctgtag----------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pu7631/1100 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggattatcatatttaaccagagaggatttcggaggaatcat-------------------- ->Am31481/110 -tctttctctccatgtcggccttgccttgttctgcttgtaaggctttcctcataccaaaagctacagagctctcatacagggtctggtaggcagcgatcgtcatacggatctcatcacgaacacgtagtaacaacaaacctcgctcagcacagttaatggtcacttggcgaatcaactcgtcaaagcattgcgaatagagctctcgtctgaccggacagattcctgtttcccgggcctgtctctgctgtagacgtctatccagttcctcctgtagattgactacgtctagacgtgtagccaccttgagagcacgcgcccttggtgttttcttgtctgtattcctgctaacaagaacaggattgtcatatttcaccagagatgcgtttggaggaatcattttgatttttgtcgggtttt
--- a/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te26821/110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt------------------------------------------------------------------- ->Ph73091/110 --------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 ----------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaataaag---------- ->Ac28061/110 -ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgactaaagcagcgtgttt ->Pg28571/110 ----gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac---------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +cccaatcgctgtcactgctctcgaagttgacattttgctgcttcatgaagaaggtcaggaattcgttgtagttgatccgtccgctgtggtccttgtcgatttcgtggacgatctgaaagagctcgtctggattgaggaaggtgttcatctcccggaagatggcgttgatctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtttgaattgggccttgagctgtttgcccttgaccttgtagcccttggccttcagggcctttttcagctccttgaaggtca +>Ac1013_1/1_1.000_525 +cccagtcgctgtcgctgctctcaaagttgacattttgctgcttcatgaagaaggtcaagaattcgtcgtagttgatccgtccgctgtggtccttgtcgatggcgtggacgatcttgaagagctcgtctggatcaaggaaggtgttcatctcttggaaaatggcgttaacctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtttgaattgagccttgagttgtttgcccttgaccttgtagcctttggccttgagggcttttttcagctccttgaaggtca
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +----------------------------------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag------------------------------------------------------------- +>Ap5050_1/1_1.000_243 +ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttctgaccttccccaagc +>Ac2173_1/1_1.000_330 +ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttctgaccttctccaagc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- a/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap5072_1/1_1.000_437 -SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV ->Ac1013_1/1_1.000_525 -PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- a/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->Am3527_1/1_1.000_270 -???????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT???????????????? ->Ap5050_1/1_1.000_243 -EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF ->Ac2173_1/1_1.000_330 -EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- a/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -1,4 +1,4 @@ ->Ac6688_1/1_1.000_963 -GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR ->Ap1491_1/1_1.000_963 -GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR +>Ap5072_1/1_1.000_437 +SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV +>Ac1013_1/1_1.000_525 +PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +???????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT???????????????? +>Ap5050_1/1_1.000_243 +EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF +>Ac2173_1/1_1.000_330 +EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_1_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +?????????????????????????????????????????????????????????????VFLVVFH +>Ap2303_1/1_1.000_424 +???????????????FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN +>Ac3644_1/1_1.000_1626 +QFIFTLFLVVIQSPHFNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN
--- a/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 -??????????????????????????????????????????????????? ->Te17661/110 -??????????????????????????????????????????????????? ->Ap26441/110 -??????????????????????????????????????????????????? ->Th39471/110 -??????????????????????????????????????????????????? ->Pf20921/110 -??????????????LSSFQKRRCSHT????????????????????LAQRS ->Pu7631/1100 -??????????????????????????????????????????????????? ->Am31481/110 -SFSPCRPCLVLLVRLSSYQKLQSSHTGSGRQRSSYGSHHEHVVTTNLAQHS
--- a/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -??????????????????????????????????????????????????FANKQM????????????????????????????????????????????????????????????????????? ->Te26821/110 -???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY?????????????????? ->Ph73091/110 -?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA????????????????????????????????????????????????????????????????????????? ->Am30661/110 -???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE ->Ac28061/110 -PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Pg28571/110 -?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV +>Ac1013_1/1_1.000_525 +PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +???????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT???????????????? +>Ap5050_1/1_1.000_243 +EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF +>Ac2173_1/1_1.000_330 +EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- a/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap5072_1/1_1.000_437 -tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt ->Ac1013_1/1_1.000_525 -cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- a/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->Am3527_1/1_1.000_270 --------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag---------------------------------------------- ->Ap5050_1/1_1.000_243 -gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc ->Ac2173_1/1_1.000_330 -gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- a/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -1,4 +1,4 @@ ->Ac6688_1/1_1.000_963 -ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg ->Ap1491_1/1_1.000_963 -ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga +>Ap5072_1/1_1.000_437 +tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt +>Ac1013_1/1_1.000_525 +cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +-------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag---------------------------------------------- +>Ap5050_1/1_1.000_243 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc +>Ac2173_1/1_1.000_330 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_1_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gggtttttcttgtagtattccac +>Ap2303_1/1_1.000_424 +--------------------------------------------ctttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaac +>Ac3644_1/1_1.000_1626 +cagttcatcttcacgttgtttcttgtagtcatacaaagccctcactttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaac
--- a/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te17661/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Ap26441/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Th39471/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pf20921/110 ------------------------------------------gctttcctcattccaaaagcgacgctgctctcataca-----------------------------------------------------------cctcgctcagcgcagt ->Pu7631/1100 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am31481/110 -tctttctctccatgtcggccttgccttgttctgcttgtaaggctttcctcataccaaaagctacagagctctcatacagggtctggtaggcagcgatcgtcatacggatctcatcacgaacacgtagtaacaacaaacctcgctcagcacagt
--- a/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te26821/110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt---------------------------------------------------- ->Ph73091/110 --------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 ----------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaa ->Ac28061/110 -ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac ->Pg28571/110 ----gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt +>Ac1013_1/1_1.000_525 +cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +-------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag---------------------------------------------- +>Ap5050_1/1_1.000_243 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc +>Ac2173_1/1_1.000_330 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- a/test-data/outputs_ORF_Search_06_CDS_with_M_aa/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ac6688_1/1_1.000_963 -GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR ->Ap1491_1/1_1.000_963 -GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- a/test-data/outputs_ORF_Search_06_CDS_with_M_aa/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -??????????????????????????????????????????????????FANKQM????????????????????????????????????????????????????????????????????? ->Te26821/110 -???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY?????????????????? ->Ph73091/110 -?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA????????????????????????????????????????????????????????????????????????? ->Am30661/110 -???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE ->Ac28061/110 -PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Pg28571/110 -?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD
--- a/test-data/outputs_ORF_Search_06_CDS_with_M_nuc/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ac6688_1/1_1.000_963 -ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg ->Ap1491_1/1_1.000_963 -ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- a/test-data/outputs_ORF_Search_06_CDS_with_M_nuc/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te26821/110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt---------------------------------------------------- ->Ph73091/110 --------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 ----------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaa ->Ac28061/110 -ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac ->Pg28571/110 ----gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_1_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_1_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -1,4 +1,4 @@ ->Ac6688_1/1_1.000_963 -GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR ->Ap1491_1/1_1.000_963 -GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR +>Ap2303_1/1_1.000_424 +FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN +>Ac3644_1/1_1.000_1626 +FNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap2303_1/1_1.000_424 -FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN ->Ac3644_1/1_1.000_1626 -FNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->Am3527_1/1_1.000_270 --------------------VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT---------------- ->Ap5050_1/1_1.000_243 -EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF ->Ac2173_1/1_1.000_330 -EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_4_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap5072_1/1_1.000_437 -SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV ->Ac1013_1/1_1.000_525 -PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV +>Ac1013_1/1_1.000_525 +PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +-------------------VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT---------------- +>Ap5050_1/1_1.000_243 +EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF +>Ac2173_1/1_1.000_330 +EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test2/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test2/orthogroup_1_with_4_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->Ac28061/110 -EAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Pg28571/110 -EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Ph73091/110 -----RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA------------------------------------------------------------------------- ->Am30661/110 -----------KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK---------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_1_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_1_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -1,4 +1,4 @@ ->Ac6688_1/1_1.000_963 -ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg ->Ap1491_1/1_1.000_963 -ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga +>Ap2303_1/1_1.000_424 +tttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaac +>Ac3644_1/1_1.000_1626 +tttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaac
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap2303_1/1_1.000_424 -tttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaac ->Ac3644_1/1_1.000_1626 -tttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaac
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ ->Am3527_1/1_1.000_270 ----------------------------------------------------------gtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacg------------------------------------------------ ->Ap5050_1/1_1.000_243 -gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc ->Ac2173_1/1_1.000_330 -gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_4_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ ->Ap5072_1/1_1.000_437 -tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt ->Ac1013_1/1_1.000_525 -cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_6_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt +>Ac1013_1/1_1.000_525 +cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_7_with_3_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +---------------------------------------------------------gtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacg------------------------------------------------ +>Ap5050_1/1_1.000_243 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc +>Ac2173_1/1_1.000_330 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test2/orthogroup_14_with_2_species.fasta Tue Jul 03 10:54:18 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- a/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test2/orthogroup_1_with_4_species.fasta Mon Mar 12 06:30:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->Ac28061/110 -gaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac ->Pg28571/110 -gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac ->Ph73091/110 -------------cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 -------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag---------------------------------------------------------------------------------------------------------------------------------------------------------