Mercurial > repos > abims-sbr > mutcount
changeset 4:5766f80370e7 draft
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 17acd02c547bd1f7661a846661aa99de9743efe9
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--- a/MutCount.xml Wed Jan 17 11:35:37 2018 -0500 +++ b/MutCount.xml Tue Feb 27 08:43:50 2018 -0500 @@ -89,7 +89,7 @@ <data format="csv" name="aatypes_counts" label="aatypes_counts.csv" from_work_dir="aatypes_counts.csv" > <filter>(method['method_run']=='concat')</filter> </data> - <data format="csv" name="gc_counts" label="codons_counts.csv" from_work_dir="gc_counts.csv" > + <data format="csv" name="gc_counts" label="gc_counts.csv" from_work_dir="gc_counts.csv" > <filter>(method['method_run']=='concat')</filter> </data> <data format="csv" name="aa_transitions" label="aa_transitions.csv" from_work_dir="aa_transitions.csv" > @@ -180,10 +180,26 @@ <param name="sep_file" ftype="fasta" value="sep_nuc/locus1_sp6_sp6.fasta,sep_nuc/locus1_sp8_sp8.fasta,sep_nuc/locus2_sp6_sp6.fasta" /> <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> </conditional> - <output name="nuc_comp" value="OUT_nuc/nuc_compositions.csv" lines_diff="2"/> - <output name="percent_gc" value="OUT_nuc/percent_GC.csv" lines_diff="2"/> - <output name="percent_pur" value="OUT_nuc/percent_purine.csv" lines_diff="2"/> - <output name="purine_load" value="OUT_nuc/Purine_Load_Indice.csv" lines_diff="2"/> + <output name="nuc_comp"> + <assert_contents> + <has_line line="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"/> + </assert_contents> + </output> + <output name="percent_gc"> + <assert_contents> + <has_line line="locus2_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="locus2_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="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" /> + </assert_contents> + </output> </test> <test> @@ -193,10 +209,26 @@ <param name="sep_file" ftype="fasta" value="sep_aa/locus1_sp6_sp6.fasta,sep_aa/locus1_sp8_sp8.fasta,sep_aa/locus2_sp6_sp6.fasta" /> <param name="concat_phy" ftype="fasta" value="phylogeny_concat.fasta" /> </conditional> - <output name="ivywrel" value="OUT_aa/IVYWREL.csv" lines_diff="2"/> - <output name="rhkde" value="OUT_aa/RHKDE.csv" lines_diff="2"/> - <output name="payre_mvgds" value="OUT_aa/PAYRE-MVGDS.csv" lines_diff="2"/> - <output name="avlimfyw" value="OUT_aa/AVLIMFYW.csv" lines_diff="2"/> + <output name="ivywrel"> + <assert_contents> + <has_line line="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" /> + </assert_contents> + </output> + <output name="rhkde"> + <assert_contents> + <has_line line="locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,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"/> + </assert_contents> + </output> + <output name="payre_mvgds"> + <assert_contents> + <has_line line="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"/> + </assert_contents> + </output> + <output name="avlimfyw"> + <assert_contents> + <has_line line="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"/> + </assert_contents> + </output> </test> </tests>
--- a/scripts/S01b_study_seq_composition_aa.py Wed Jan 17 11:35:37 2018 -0500 +++ b/scripts/S01b_study_seq_composition_aa.py Tue Feb 27 08:43:50 2018 -0500 @@ -545,19 +545,19 @@ 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," %("n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a")) - fileOUT_IVYWREL.write("%s,%s," %("n.a", "n.a")) - fileOUT_ERK_DNQTSH.write("%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a")) - fileOUT_EK_QH.write("%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a")) - fileOUT_FYMINK_GARP.write("%s,%s,%s,%s," %("n.a","n.a","n.a","n.a")) - fileOUT_AVLIMFYW.write("%s,%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a","n.a")) - fileOUT_STNQ.write("%s,%s," %("n.a","n.a")) - fileOUT_RHKDE.write("%s,%s,%s,%s,%s,%s,"%("n.a","n.a","n.a","n.a","n.a","n.a")) - fileOUT_PAYRE.write("%s,%s,%s,%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a","n.a","n.a","n.a")) - fileOUT_TotalResidueWeight.write("%s," %"n.a") - fileOUT_TotalResidueVolume.write("%s," %"n.a") - fileOUT_TotalPartialSpecificVolume.write("%s," %"n.a") - fileOUT_TotalHydratation.write("%s," %"n.a") + 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")
--- a/scripts/S02a_codon_counting.py Wed Jan 17 11:35:37 2018 -0500 +++ b/scripts/S02a_codon_counting.py Tue Feb 27 08:43:50 2018 -0500 @@ -136,6 +136,7 @@ maxval=iterration-1 minval=0 testval=(maxval+minval)/2 + print bootstrap[testval] while maxval-minval > 1: if value > bootstrap[testval]: minval=testval @@ -673,9 +674,10 @@ gc_counts.write(",") gc_counts.write(str(GC3_b)+","+str(GC12_b)+","+str(IVYWREL_b)+","+str(EKQH_b)+","+str(PAYRESDGM_b)+","+str(purineload_b)+","+str(CvP_b)) - # end writing + # end writing stringcounts=stringcounts[:-1]+[''.join([stringcounts[-1],("counting of %s\n\n" % p[0])+''.join(strcountings(codonscount, aacount, aaclassifcount,codonscountpvalue,aacountpvalue,aaclassifcountpvalue,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP))+'\n\n'])] + else: towrite=1 # -----------------------------
--- a/scripts/S02b_study_seq_composition_nuc.py Wed Jan 17 11:35:37 2018 -0500 +++ b/scripts/S02b_study_seq_composition_nuc.py Tue Feb 27 08:43:50 2018 -0500 @@ -170,10 +170,10 @@ 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," %("n.a","n.a","n.a","n.a")) - fileOUT_percent_GC.write("%s," %"n.a") - fileOUT_percent_purine.write("%s," %"n.a") - fileOUT_Purine_Load.write("%s,%s,%s,%s,%s," %("n.a","n.a","n.a","n.a","n.a")) + 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")
--- a/test-data/OUT_aa/AVLIMFYW.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/AVLIMFYW.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,n.a,n.a,n.a,n.a,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,n.a,n.a,n.a,n.a,n.a,n.a,28.00000,0.43750,22.00000,0.34375,6.00000,0.09375,30.00000,0.46875,24.00000,0.37500,6.00000,0.09375,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,24.00000,0.30769,22.00000,0.28205,2.00000,0.02564, -locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,28.00000,0.36364,25.00000,0.32468,3.00000,0.03896,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/EK_QH.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,n.a,n.a,n.a,13.00000,0.20312,2.00000,0.03125,6.50000,n.a,n.a,n.a,n.a,n.a,14.00000,0.21875,2.00000,0.03125,7.00000,13.00000,0.20312,2.00000,0.03125,6.50000,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,10.00000,0.12821,11.00000,0.14103,0.90909, -locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,10.00000,0.12987,5.00000,0.06494,2.00000,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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,0.00000,0.00000,0.00000,0.00000,0.00000,10.00000,0.12987,5.00000,0.06494,2.00000,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/ERK_DNQTSH.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,n.a,n.a,n.a,13.00000,0.20312,13.00000,0.20312,1.00000,n.a,n.a,n.a,n.a,n.a,14.00000,0.21875,13.00000,0.20312,1.07692,13.00000,0.20312,14.00000,0.21875,0.92857,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,17.00000,0.21795,31.00000,0.39744,0.54839, -locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,11.00000,0.14286,31.00000,0.40260,0.35484,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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,0.00000,0.00000,0.00000,0.00000,0.00000,11.00000,0.14286,31.00000,0.40260,0.35484,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/FYMINK_GARP.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,n.a,n.a,21.00000,0.32812,16.00000,0.25000,n.a,n.a,n.a,n.a,21.00000,0.32812,15.00000,0.23438,20.00000,0.31250,15.00000,0.23438,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,13.00000,0.16667,19.00000,0.24359,13.00000,0.16667,18.00000,0.23077,12.00000,0.15385,18.00000,0.23077,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,13.00000,0.16667,18.00000,0.23077, -locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,16.00000,0.20779,12.00000,0.15584,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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,0.00000,0.00000,0.00000,0.00000,16.00000,0.20779,12.00000,0.15584,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/IVYWREL.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,23.00000,0.35938,n.a,n.a,22.00000,0.34375,23.00000,0.35938,n.a,n.a,n.a,n.a,22.00000,0.34375, -locus1_sp6_sp6.fasta,29.00000,0.37179,31.00000,0.39744,n.a,n.a,n.a,n.a,29.00000,0.37179,28.00000,0.35897,29.00000,0.37179,n.a,n.a,n.a,n.a,28.00000,0.35897, -locus1_sp8_sp8.fasta,0.00000,0.00000,28.00000,0.36364,n.a,n.a,n.a,n.a,27.00000,0.35065,27.00000,0.35065,28.00000,0.36364,0.00000,0.00000,27.00000,0.40909,27.00000,0.35065, +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,0.00000,0.00000,28.00000,0.36364,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/PAYRE-MVGDS.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,18.00000,0.28125,6.00000,0.09375,20.00000,0.31250,0.90000,0.30000,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,24.00000,0.30769,7.00000,0.08974,22.00000,0.28205,1.09091,0.31818, -locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,18.00000,0.23377,4.00000,0.05195,29.00000,0.37662,0.62069,0.13793,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/RHKDE.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,n.a,n.a,n.a,n.a,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,n.a,n.a,n.a,n.a,n.a,n.a,20.00000,0.31250,10.00000,0.15625,10.00000,0.15625,19.00000,0.29688,9.00000,0.14062,10.00000,0.15625,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,30.00000,0.38462,16.00000,0.20513,14.00000,0.17949, -locus1_sp8_sp8.fasta,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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,0.00000,0.00000,0.00000,0.00000,0.00000,0.00000,14.00000,0.18182,4.00000,0.05195,10.00000,0.12987,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/STNQ.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,n.a,7.00000,0.10938,n.a,n.a,7.00000,0.10938,8.00000,0.12500,n.a,n.a,n.a,n.a,7.00000,0.10938, -locus1_sp6_sp6.fasta,19.00000,0.24359,15.00000,0.19231,n.a,n.a,n.a,n.a,18.00000,0.23077,18.00000,0.23077,18.00000,0.23077,n.a,n.a,n.a,n.a,18.00000,0.23077, -locus1_sp8_sp8.fasta,0.00000,0.00000,28.00000,0.36364,n.a,n.a,n.a,n.a,27.00000,0.35065,25.00000,0.32468,27.00000,0.35065,0.00000,0.00000,24.00000,0.36364,26.00000,0.33766, +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,0.00000,0.00000,28.00000,0.36364,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 Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/TotalHydratation.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,170.50000,n.a,171.00000,171.50000,n.a,n.a,171.00000, -locus1_sp6_sp6.fasta,224.00000,224.50000,n.a,n.a,223.00000,226.00000,226.00000,n.a,n.a,226.00000, -locus1_sp8_sp8.fasta,0.00000,188.00000,n.a,n.a,190.50000,188.50000,192.00000,0.00000,167.50000,189.50000, +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,0.00000,188.00000,NA,NA,190.50000,188.50000,192.00000,0.00000,167.50000,189.50000,
--- a/test-data/OUT_aa/TotalPartialSpecificVolume.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/TotalPartialSpecificVolume.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,47.71000,n.a,48.17000,47.97000,n.a,n.a,48.17000, -locus1_sp6_sp6.fasta,56.53000,56.56000,n.a,n.a,56.37000,56.43000,56.54000,n.a,n.a,56.43000, -locus1_sp8_sp8.fasta,0.00000,56.86000,n.a,n.a,56.93000,57.09000,56.25000,0.00000,49.09000,57.05000, +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,0.00000,56.86000,NA,NA,56.93000,57.09000,56.25000,0.00000,49.09000,57.05000,
--- a/test-data/OUT_aa/TotalResidueVolume.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/TotalResidueVolume.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,6587.00000,n.a,6645.00000,6631.00000,n.a,n.a,6645.00000, -locus1_sp6_sp6.fasta,8265.00000,8257.00000,n.a,n.a,8305.00000,8257.00000,8277.00000,n.a,n.a,8257.00000, -locus1_sp8_sp8.fasta,0.00000,7671.00000,n.a,n.a,7642.00000,7493.00000,7561.00000,0.00000,6633.00000,7519.00000, +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,0.00000,7671.00000,NA,NA,7642.00000,7493.00000,7561.00000,0.00000,6633.00000,7519.00000,
--- a/test-data/OUT_aa/TotalResidueWeight.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/TotalResidueWeight.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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,n.a,6961.51000,n.a,6990.69000,7005.54000,n.a,n.a,6990.69000, -locus1_sp6_sp6.fasta,8981.54000,8937.66000,n.a,n.a,9023.69000,8989.64000,8985.64000,n.a,n.a,8989.64000, -locus1_sp8_sp8.fasta,0.00000,8270.91000,n.a,n.a,8248.86000,8082.66000,8213.63000,0.00000,7124.55000,8112.69000, +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,0.00000,8270.91000,NA,NA,8248.86000,8082.66000,8213.63000,0.00000,7124.55000,8112.69000,
--- a/test-data/OUT_aa/prot_compositions_All_AA.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_aa/prot_compositions_All_AA.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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, 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--- a/test-data/OUT_nuc/Purine_Load_Indice.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_nuc/Purine_Load_Indice.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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, -locus2_sp6_sp6.fasta,192,12,12,62.50000,62.50000,192,12,4,62.50000,20.83333,n.a,n.a,n.a,n.a,n.a,192,11,11,57.29167,57.29167,n.a,n.a,n.a,n.a,n.a,192,16,10,83.33333,52.08333,192,10,20,52.08333,104.16667,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,192,14,12,72.91667,62.50000, -locus1_sp6_sp6.fasta,234,2,28,8.54701,119.65812,234,6,20,25.64103,85.47009,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,234,18,20,76.92308,85.47009,234,0,24,0.00000,102.56410,234,8,16,34.18803,68.37607,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,234,-1,23,-4.27350,98.29060, -locus1_sp8_sp8.fasta,198,6,20,30.30303,101.01010,231,4,19,17.31602,82.25108,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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, +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, +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,
--- a/test-data/OUT_nuc/nuc_compositions.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_nuc/nuc_compositions.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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, -locus2_sp6_sp6.fasta,0.30208,0.23958,0.19792,0.26042,0.29688,0.27604,0.18229,0.24479,n.a,n.a,n.a,n.a,0.30208,0.24479,0.19792,0.25521,n.a,n.a,n.a,n.a,0.31250,0.26042,0.17188,0.25521,0.32292,0.21875,0.20312,0.25521,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,0.31771,0.25521,0.17708,0.25000, -locus1_sp6_sp6.fasta,0.33761,0.21795,0.21795,0.22650,0.28632,0.20085,0.24359,0.26923,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,0.29915,0.21368,0.20513,0.28205,0.31624,0.21368,0.23504,0.23504,0.30342,0.23504,0.21368,0.24786,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,0.31624,0.21795,0.23504,0.23077, -locus1_sp8_sp8.fasta,0.33333,0.23232,0.20202,0.23232,0.32468,0.24242,0.20779,0.22511,n.a,n.a,n.a,n.a,n.a,n.a,n.a,n.a,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, +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, +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, +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,
--- a/test-data/OUT_nuc/percent_GC.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_nuc/percent_GC.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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_percent_GC, -locus2_sp6_sp6.fasta,45.83333,42.70833,n.a,45.31250,n.a,42.70833,45.83333,n.a,n.a,42.70833, -locus1_sp6_sp6.fasta,44.44444,51.28205,n.a,n.a,48.71795,47.00855,46.15385,n.a,n.a,46.58120, -locus1_sp8_sp8.fasta,43.43434,43.29004,n.a,n.a,43.29004,44.58874,40.25974,0.00000,38.38384,44.58874, +locus2_sp6_sp6.fasta,45.83333,42.70833,NA,45.31250,NA,42.70833,45.83333,NA,NA,42.70833, +locus1_sp6_sp6.fasta,44.44444,51.28205,NA,NA,48.71795,47.00855,46.15385,NA,NA,46.58120, +locus1_sp8_sp8.fasta,43.43434,43.29004,NA,NA,43.29004,44.58874,40.25974,0.00000,38.38384,44.58874,
--- a/test-data/OUT_nuc/percent_purine.csv Wed Jan 17 11:35:37 2018 -0500 +++ b/test-data/OUT_nuc/percent_purine.csv Tue Feb 27 08:43:50 2018 -0500 @@ -1,4 +1,4 @@ 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, -locus2_sp6_sp6.fasta,56.25000,54.16667,n.a,55.72917,n.a,56.77083,57.81250,n.a,n.a,56.77083, -locus1_sp6_sp6.fasta,56.41026,55.55556,n.a,n.a,58.11966,55.12821,55.12821,n.a,n.a,54.70085, -locus1_sp8_sp8.fasta,56.56566,54.97835,n.a,n.a,55.84416,54.97835,56.27706,0.00000,56.06061,54.97835, +locus2_sp6_sp6.fasta,56.25000,54.16667,NA,55.72917,NA,56.77083,57.81250,NA,NA,56.77083, +locus1_sp6_sp6.fasta,56.41026,55.55556,NA,NA,58.11966,55.12821,55.12821,NA,NA,54.70085, +locus1_sp8_sp8.fasta,56.56566,54.97835,NA,NA,55.84416,54.97835,56.27706,0.00000,56.06061,54.97835,