Mercurial > repos > abims-sbr > mutcount
changeset 0:acc3674e515b draft default tip
planemo upload for repository htpps://github.com/abims-sbr/adaptearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MutCount.xml Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,424 @@ +<?xml version="1.0"?> + +<tool name="MutCount" id="mutcount" version="2.2.0"> + <description> + This tool proceeds to count codons, amino acids on each species of a set of species, and then proceeds to permutation tests. + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + <expand macro="python_required" /> + <requirement type="package" version="0.20.0">pandas</requirement> + <requirement type="package" version="1.12.0">numpy</requirement> + <requirement type="package" version="1.4.4">r-optparse</requirement> + </requirements> + + <command> + <![CDATA[ + + ln -s $__tool_directory__/scripts/functions.py . && + + #if str($method.method_run) == "concat" : + python '$__tool_directory__/scripts/S01a_codons_counting.py' ${method.concat_nuc} '$method.list_species' '$method.list_species_boot' $method.num_iter $method.num_sampled > ${log} + #end if + + #if str($method.method_run) == "separated" : + mkdir 01_input_files && + ln -s '$__tool_directory__/scripts/S03b_sign_test_binomial.R' . && + #for $input in $method.sep_file + ln -s '$input' '01_input_files/$input.element_identifier'; + #end for + + #if str($method.format_run)== "nucleic" : + python '$__tool_directory__/scripts/S01b_extract_variable_nuc.py' ${method.sps_list} && + #end if + + #if str($method.format_run)== "proteic" : + cp '$__tool_directory__/scripts/amino_acid_properties.csv' . && + python '$__tool_directory__/scripts/S01b_extract_variable_prot.py' ${method.sps_list} amino_acid_properties.csv && + #end if + + python '$__tool_directory__/scripts/S02b_extreme_2states.py' ${method.sps_gp1} ${method.sps_gp2} ${method.format_run} + #end if + + ]]> + </command> + + <inputs> + <conditional name="method"> + <param name="method_run" type="select" label="Which method do you want to use for this tool? "> + <option value="concat">Concatenated genes in DNA (concatenation from RAxML run)</option> + <option value="separated">Set of separated genes (from ORF_Search output "output zip containing files with CDS without indel")</option> + </param> + + <when value="concat"> + <param name="concat_nuc" type="data" format="fasta" label="Choose your fasta file in nucleic format" help="It must contain the concatenated file in NUCLEIC format from Phylogeny tool" /> + <param name="list_species" type="text" size="100" label="List of species for countings" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" /> + <param name="list_species_boot" type="text" size="100" label="List of species (at least two) used for resampling" help="List the species separated with a comma (for e.g Ap,As,Ct,Gt,Yu)" /> + <param name="num_iter" type="integer" value="1000" min="0" label="Number of sampled codons" help="Sets the length (in codons) of the resampled sequences"/> + <param name="num_sampled" type="integer" value="1000" min="0" label="Number of iterations" help="Sets the number of resampled sequences"/> + </when> + + <when value="separated"> + <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? "> + <option value="nucleic">Nucleic format</option> + <option value="proteic">Proteic format</option> + </param> + <param name="sep_file" type="data" format="fasta" multiple="true" label="Choose fasta files" help="Fasta files from ORF_search tool ; in nucleic or proteic, according to the format chosen above" /> + <param name="sps_list" type="text" size="100" label="Enter all the studied species" help="Enter all the species present in the set of fasta files (comma-separated abbreviated names)" /> + <param name="sps_gp1" type="text" size="100" label="Species for group one" help="Specify species (comma-separated abbreviated names) sharing an ecological condition"/> + <param name="sps_gp2" type="text" size="100" label="Species for group two" help="Specify species (comma-separated abbreviated names) sharing an other ecological condition"/> + </when> + </conditional> + </inputs> + + <outputs> + <!-- output concat --> + <data format="txt" name="log" label="MutCount_concat_log.output" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="codons_freqs" label="codons_freqs.csv" from_work_dir="codons_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="aa_freqs" label="aa_freqs.csv" from_work_dir="aa_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="aatypes_freqs" label="aatypes_freqs.csv" from_work_dir="aatypes_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="gc_and_others_freqs" label="gc_and_others_freqs.csv" from_work_dir="gc_and_others_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="codons_transitions_freqs" label="codons_transitions_freqs" from_work_dir="codons_transitions_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="aa_transitions_freqs" label="aa_transitions_freqs.csv" from_work_dir="aa_transitions_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + <data format="csv" name="aatypes_transitions_freqs" label="aatypes_transitions.csv" from_work_dir="aatypes_transitions_freqs.csv" > + <filter>(method['method_run']=='concat')</filter> + </data> + + <!-- outputs separated - nucleic --> + <collection name="tables_nuc" type="list" label="counts_on_nucleotides"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_nucleotide" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> + </collection> + <collection name="tables_nuc_var" type="list" label="counts_on_nuc_variables"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_nuc_variable" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> + </collection> + <collection name="outputs_nuc" type="list" label="binomial_tests_on_nucleotides"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_nucleotides" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> + </collection> + <collection name="outputs_nuc_var" type="list" label="binomial_tests_on_nuc_variables"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_nuc_variables" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'nucleic')</filter> + </collection> + + <!-- outputs separated - proteic --> + <collection name="tables_aa" type="list" label="counts_on_amino_acids"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_aa" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> + </collection> + <collection name="tables_variables" type="list" label="counts_on_indices"> + <discover_datasets pattern="__name_and_ext__" directory="02_tables_per_aa_variable" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> + </collection> + <collection name="outputs_aa" type="list" label="binomial_tests_on_amino_acids"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_aa" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> + </collection> + <collection name="outputs_variables" type="list" label="binomial_tests_on_indices"> + <discover_datasets pattern="__name_and_ext__" directory="04_outputs_aa_variables" /> + <filter>(method['method_run']=='separated' and method['format_run']== 'proteic')</filter> + </collection> + </outputs> + + <tests> + + <test> + <conditional name="method" > + <param name="method_run" value="concat" /> + <param name="concat_nuc" ftype="fasta" value="concatenation.fasta" /> + <param name="list_species" ftype="text" value="Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi" /> + <param name="list_species_boot" ftype="text" value="Ps,Pp,Pu,Pf" /> + <param name="num_iter" value="200" /> + <param name="num_sampled" value="200" /> + </conditional> + <output name="log" value="OUT_concat/MutCount_concat_log.output" lines_diff="2"/> + <output name="codons_freqs" value="OUT_concat/codons_freqs.csv" lines_diff="18"/> + <output name="aa_freqs" value="OUT_concat/aa_freqs.csv" lines_diff="18"/> + <output name="aatypes_freqs" value="OUT_concat/aatypes_freqs.csv" lines_diff="18"/> + <output name="gc_and_others_freqs" value="OUT_concat/gc_and_others_freqs.csv"/> + <output name="codons_transitions_freqs" value="OUT_concat/codons_transitions_freqs.csv" lines_diff="72"/> + <output name="aa_transitions_freqs" value="OUT_concat/aa_transitions_freqs.csv" lines_diff="72"/> + <output name="aatypes_transitions_freqs" value="OUT_concat/aatypes_transitions_freqs.csv" lines_diff="72"/> + </test> + + <test> + <conditional name="method" > + <param name="method_run" value="separated" /> + <param name="format_run" value="nucleic" /> + <param name="sep_file" ftype="fasta" value="sep_nuc/orthogroup_109_with_3_species.fasta,sep_nuc/orthogroup_113_with_4_species.fasta,sep_nuc/orthogroup_253_with_2_species.fasta,sep_nuc/orthogroup_283_with_2_species.fasta,sep_nuc/orthogroup_299_with_2_species.fasta,sep_nuc/orthogroup_301_with_4_species.fasta,sep_nuc/orthogroup_316_with_4_species.fasta,sep_nuc/orthogroup_335_with_4_species.fasta,sep_nuc/orthogroup_343_with_4_species.fasta,sep_nuc/orthogroup_368_with_4_species.fasta,sep_nuc/orthogroup_404_with_4_species.fasta,sep_nuc/orthogroup_442_with_4_species.fasta,sep_nuc/orthogroup_487_with_4_species.fasta,sep_nuc/orthogroup_508_with_4_species.fasta,sep_nuc/orthogroup_544_with_4_species.fasta,sep_nuc/orthogroup_546_with_4_species.fasta,sep_nuc/orthogroup_588_with_4_species.fasta,sep_nuc/orthogroup_623_with_4_species.fasta,sep_nuc/orthogroup_651_with_4_species.fasta,sep_nuc/orthogroup_660_with_4_species.fasta,sep_nuc/orthogroup_696_with_4_species.fasta,sep_nuc/orthogroup_707_with_4_species.fasta,sep_nuc/orthogroup_727_with_4_species.fasta,sep_nuc/orthogroup_761_with_4_species.fasta" /> + <param name="sps_list" value="Ha,Lf,Bs,Bj" /> + <param name="sps_gp1" value="Ha,Lf" /> + <param name="sps_gp2" value="Bs,Bj" /> + </conditional> + <output_collection name="tables_nuc" type="list" count="4"> + <element name="A" file="OUT_nuc/02_tables_per_nucleotide/A.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="C" file="OUT_nuc/02_tables_per_nucleotide/C.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="G" file="OUT_nuc/02_tables_per_nucleotide/G.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="T" file="OUT_nuc/02_tables_per_nucleotide/T.csv" ftype="csv" compare="diff" lines_diff="8" /> + </output_collection> + <output_collection name="tables_nuc_var" type="list" count="8"> + <element name="DIFF_AT" file="OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DIFF_GC" file="OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="GC_percent" file="OUT_nuc/02_tables_per_nuc_variable/_GC_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="PLI_AT" file="OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_AT_1000" file="OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC" file="OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC_1000" file="OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="purine_percent" file="OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="outputs_nuc" type="list" count="4"> + <element name="A" file="OUT_nuc/04_outputs_nucleotides/A.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="C" file="OUT_nuc/04_outputs_nucleotides/C.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="G" file="OUT_nuc/04_outputs_nucleotides/G.csv" ftype="csv" compare="diff" lines_diff="8" /> + <element name="T" file="OUT_nuc/04_outputs_nucleotides/T.csv" ftype="csv" compare="diff" lines_diff="8" /> + </output_collection> + <output_collection name="outputs_nuc_var" type="list" count="8"> + <element name="DIFF_AT" file="OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DIFF_GC" file="OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="GC_percent" file="OUT_nuc/04_outputs_nuc_variables/GC_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="PLI_AT" file="OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_AT_1000" file="OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC" file="OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="PLI_GC_1000" file="OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="purine_percent" file="OUT_nuc/04_outputs_nuc_variables/purine_percent.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + </test> + + <test> + <conditional name="method" > + <param name="method_run" value="separated" /> + <param name="format_run" value="proteic" /> + <param name="sep_file" ftype="fasta" value="sep_aa/locus_3sp_2.fasta,sep_aa/locus_3sp_7.fasta,sep_aa/locus_4sp_4.fasta,sep_aa/locus_4sp_6.fasta,sep_aa/locus_6sp_10.fasta,sep_aa/locus_6sp_11.fasta,sep_aa/locus_6sp_16.fasta,sep_aa/locus_6sp_18.fasta,sep_aa/locus_6sp_25.fasta,sep_aa/locus_6sp_27.fasta,sep_aa/locus_6sp_30.fasta,sep_aa/locus_6sp_32.fasta,sep_aa/locus_6sp_35.fasta,sep_aa/locus_6sp_38.fasta,sep_aa/locus_6sp_39.fasta,sep_aa/locus_6sp_40.fasta,sep_aa/locus_6sp_41.fasta,sep_aa/locus_6sp_46.fasta,sep_aa/locus_6sp_47.fasta,sep_aa/locus_6sp_50.fasta,sep_aa/locus_6sp_53.fasta,sep_aa/locus_6sp_57.fasta,sep_aa/locus_6sp_58.fasta,sep_aa/locus_6sp_60.fasta" /> + <param name="sps_list" value="Ps,Pp,Pf,Ac,Pg,Ap" /> + <param name="sps_gp1" value="Pp,Pg" /> + <param name="sps_gp2" value="Ap,Ps" /> + </conditional> + <output_collection name="tables_aa" type="list" count="20"> + <element name="A" file="OUT_aa/02_tables_per_aa/A.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="C" file="OUT_aa/02_tables_per_aa/C.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="D" file="OUT_aa/02_tables_per_aa/D.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="E" file="OUT_aa/02_tables_per_aa/E.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="F" file="OUT_aa/02_tables_per_aa/F.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="G" file="OUT_aa/02_tables_per_aa/G.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="H" file="OUT_aa/02_tables_per_aa/H.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="I" file="OUT_aa/02_tables_per_aa/I.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="K" file="OUT_aa/02_tables_per_aa/K.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="L" file="OUT_aa/02_tables_per_aa/L.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="M" file="OUT_aa/02_tables_per_aa/M.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="N" file="OUT_aa/02_tables_per_aa/N.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="P" file="OUT_aa/02_tables_per_aa/P.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Q" file="OUT_aa/02_tables_per_aa/Q.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="R" file="OUT_aa/02_tables_per_aa/R.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="S" file="OUT_aa/02_tables_per_aa/S.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="T" file="OUT_aa/02_tables_per_aa/T.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="V" file="OUT_aa/02_tables_per_aa/V.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="W" file="OUT_aa/02_tables_per_aa/W.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Y" file="OUT_aa/02_tables_per_aa/Y.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="tables_variables" type="list" count="26"> + + <element name="AC" file="OUT_aa/02_tables_per_aa_variable/AC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="APGC" file="OUT_aa/02_tables_per_aa_variable/APGC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIM" file="OUT_aa/02_tables_per_aa_variable/AVLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIMFYW" file="OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DE" file="OUT_aa/02_tables_per_aa_variable/DE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DNQTSHA" file="OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="EK" file="OUT_aa/02_tables_per_aa_variable/EK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ERK" file="OUT_aa/02_tables_per_aa_variable/ERK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYMINK" file="OUT_aa/02_tables_per_aa_variable/FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYW" file="OUT_aa/02_tables_per_aa_variable/FYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="GARP" file="OUT_aa/02_tables_per_aa_variable/GARP.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="IVYWREL" file="OUT_aa/02_tables_per_aa_variable/IVYWREL.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="QH" file="OUT_aa/02_tables_per_aa_variable/QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_AC_VLIM" file="OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_APGC_VLIM" file="OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_EK_QH" file="OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_ERK_DNQTSHA" file="OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_GARP_FYMINK" file="OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHK" file="OUT_aa/02_tables_per_aa_variable/RHK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHKDE" file="OUT_aa/02_tables_per_aa_variable/RHKDE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="STNQ" file="OUT_aa/02_tables_per_aa_variable/STNQ.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="total_hydratation" file="OUT_aa/02_tables_per_aa_variable/total_hydratation.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="total_partial_specific_volume" file="OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_volume" file="OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_weight" file="OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="VLIM" file="OUT_aa/02_tables_per_aa_variable/VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="outputs_aa" type="list" count="20"> + <element name="A" file="OUT_aa/04_outputs_aa/A.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="C" file="OUT_aa/04_outputs_aa/C.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="D" file="OUT_aa/04_outputs_aa/D.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="E" file="OUT_aa/04_outputs_aa/E.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="F" file="OUT_aa/04_outputs_aa/F.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="G" file="OUT_aa/04_outputs_aa/G.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="H" file="OUT_aa/04_outputs_aa/H.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="I" file="OUT_aa/04_outputs_aa/I.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="K" file="OUT_aa/04_outputs_aa/K.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="L" file="OUT_aa/04_outputs_aa/L.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="M" file="OUT_aa/04_outputs_aa/M.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="N" file="OUT_aa/04_outputs_aa/N.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="P" file="OUT_aa/04_outputs_aa/P.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Q" file="OUT_aa/04_outputs_aa/Q.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="R" file="OUT_aa/04_outputs_aa/R.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="S" file="OUT_aa/04_outputs_aa/S.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="T" file="OUT_aa/04_outputs_aa/T.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="V" file="OUT_aa/04_outputs_aa/V.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="W" file="OUT_aa/04_outputs_aa/W.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="Y" file="OUT_aa/04_outputs_aa/Y.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + <output_collection name="outputs_variables" type="list" count="26"> + <element name="AC" file="OUT_aa/04_outputs_aa_variables/AC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="APGC" file="OUT_aa/04_outputs_aa_variables/APGC.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIM" file="OUT_aa/04_outputs_aa_variables/AVLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="AVLIMFYW" file="OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DE" file="OUT_aa/04_outputs_aa_variables/DE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="DNQTSHA" file="OUT_aa/04_outputs_aa_variables/DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="EK" file="OUT_aa/04_outputs_aa_variables/EK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ERK" file="OUT_aa/04_outputs_aa_variables/ERK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYMINK" file="OUT_aa/04_outputs_aa_variables/FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="FYW" file="OUT_aa/04_outputs_aa_variables/FYW.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="GARP" file="OUT_aa/04_outputs_aa_variables/GARP.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="IVYWREL" file="OUT_aa/04_outputs_aa_variables/IVYWREL.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="QH" file="OUT_aa/04_outputs_aa_variables/QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_AC_VLIM" file="OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_APGC_VLIM" file="OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_EK_QH" file="OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_ERK_DNQTSHA" file="OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="ratio_GARP_FYMINK" file="OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHK" file="OUT_aa/04_outputs_aa_variables/RHK.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="RHKDE" file="OUT_aa/04_outputs_aa_variables/RHKDE.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="STNQ" file="OUT_aa/04_outputs_aa_variables/STNQ.csv" ftype="csv" compare="diff" lines_diff="6" /> + <!-- + <element name="total_hydratation" file="OUT_aa/04_outputs_aa_variables/total_hydratation.csv" ftype="csv" compare="diff" lines_diff="6" /> + --> + <element name="total_partial_specific_volume" file="OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_volume" file="OUT_aa/04_outputs_aa_variables/total_residue_volume.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="total_residue_weight" file="OUT_aa/04_outputs_aa_variables/total_residue_weight.csv" ftype="csv" compare="diff" lines_diff="6" /> + <element name="VLIM" file="OUT_aa/04_outputs_aa_variables/VLIM.csv" ftype="csv" compare="diff" lines_diff="6" /> + </output_collection> + </test> + + </tests> + + <help> + +@HELP_AUTHORS@ + +<![CDATA[ + +**Description** + +*1-Separated mode* + +Input files are all the orthogroups computed by the AdaptSearch suite; Counts and test are computed on each group separatly. This mode counts occurrences of amino-acids or nucleic acids, according to the sequences type, in each distinct orthogroup. Then, two subgroups of species are set by the user : + +- A first group, constitued by species having something in common (an ecological trait, an ecological niche, a particular environmental adaptation) +- A second group, constitued by species sharing the opposite trait (for example, the user can have a first subgroup made with species adapted to high temperatures and a second group made with species adapted to cold temperatures) + +Within the groups, the program checks wether the occurrences of each element (amino-acid, nucleic acid, thermostability indice, GC content …) is higher of lower between one species and all the species of the opposite group. Binomial tests are then performed of these counts. + +*2-Concatenated mode* + +The input file is the super-alignment obtained by concatenation of all the orthogroups computed by the AdaptSearch suite. This script counts the number of codons, amino acids, and types of amino acids in sequences, as well as the mutation bias from one item to another between 2 sequences. Counts are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences. + +In the output files, the pvalues indicate the position of the observed data in a distribution of empirical counts obtained from a resampling of the data. Values above 0.95 indicate a significantly higher count, values under 0.05 a significantly lower count. + +The script resamples random pairs of aligned codon to determine what counts can be expected under the hypothesis of an homogenous dataset. +Counts are performed on each generated random alignement, thousands of alignments allow to draw a gaussian distribution of the counts. +Then the script simply checks whether the observed data are within the 5% lowest or 5% highest values of the distribution. + +-------- + +.. class:: infomark + +**Input files** + +If you choose the concatenated method, the input file is the concatenated genes fasta file (in nucleic format) from a previous run of the toolConcatPhyl. + +If you choose the separated method, there are two input files : +- A dataset collection containing output files from the CDS_Search tool, the one without indels. These files must be in nucleic or proteic format according to the format chosen along with the method. +- The concatenated genes fasta file from ConcatPhyl, only used here to retrieve species name. + +-------- + +**Parameters** + +There are parameters only for the "Concatenated" method : + +- The list of species for **countings**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species, not only on the total number of species present in the previous tools. + +- The list of species for **resampling**, separated by commas and without space (e.g : sp1,sp2,sp3,sp4). You can run the tool on subgroup of species (at least two species), not only on the total number of species present in the previous tools. + +- The number of iterations : the number of alignments that will be generated (effect on the resolution of the gaussian distribution). Shouldn't be lower than 1000 to have a relatively smooth gaussian distribution. + +- The number of sampled codons : the number of pairs of codons in each generated alignments (effect on the robustness on the counts performed on this alignement). Shouldn't be lower than 1000 to detect codons with relatively low occurence (<1%). + +-------- + +**Outputs** + +Many outputs in .csv format , varying according to the chosen method and format (separated, nucleic ...) + - When method = concat : 6 .csv outputs : countings of codons, amino acids, amino acids types, and transitions from amino acid to amino acid and from amino acid type to amino acid type. + - When method = separated and format = nucleic : 4 collections with several .csv files : counts tables and binomial sign tests results for nucleotides and various indices (GC and purine percent ...) . + - When method = separated and format = proteic : 4 collections with several .csv files : counts tables and binomial sign tests results for amino-acids and various indices (thermophilic indices, hydratation, partial specific volume...). +--------- + +**The AdaptSearch Pipeline** + +.. image:: adaptsearch_picture_helps.png + +--------- + +Changelog +--------- + +**Version 2.2.0 - 10/07/2018** +- Updated separated mode : added a binomial sign test + +**Version 2.1 - 26/02/2017** +- Fully re-written the concat method : fixed mistakes + cleaner code +- Splitted output of concatenated method in several csv files. +- Bug corrected in output files of separated method. + +**Version 2.0 - 12/07/2017** + +- NEW: Replaced the zip between tools by Dataset Collection +- More functional tests + +**Version 1.0 - 14/04/2017** + +- Added the tools to the suite +- Added a functional test with planemo +- Planemo test using conda dependencies for python +- Scripts renamed + symlinks to the directory 'scripts' + + ]]> + + </help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,13 @@ +Changelog + + Version 2.0 - 12/07/2017 + + - NEW: Replaced the zip between tools by Dataset Collection + - More functional tests + + Version 1.0 - 14/04/2017 + + - Added the tools to the suite + - Added a functional test with planemo + - Planemo test using conda dependencies for python + - Scripts renamed + symlinks to the directory 'scripts'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,32 @@ +<macros> + + <xml name="python_required"> + <requirement type="package" version="2.7">python</requirement> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2. + +.. class:: infomark + +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station + + | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor + +--------------------------------------------------- + + </token> + + <xml name="citations"> + <citations> + <citation type="bibtex">Credits : ABIMS team, Roscoff Marine Station</citation> + <citation type="bibtex">Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.</citation> + <citation type="bibtex">Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard</citation> + <citation type="bibtex">Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor</citation> + </citations> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01a_codons_counting.py Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,937 @@ +#!/usr/bin/env python +# coding: utf-8 +# Author : Victor Mataigne + +import string, os, sys, re, random, itertools, argparse, copy, math +import pandas as pd +import numpy as np + +def buildDicts(list_codons, content, dict_genetic_code, dict_aa_classif): + """ Build dictionaries with values to 0. These dictionaries are used as starting point for each sequence counting + + Args : + list_codons (list of str) : all codons except codons-stop + content (int or list) : an integer (for coutings and transitions), or an empty list (for resampling) + dict_genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...} + dict_aa_classif (dict) : the types of the amino-acids ( {type: [aa1, aa2, ...], ...} + + Returns : + dico_codons, dico_aa, dico_aatypes (dicts) : keys : codons/amico-acids/amico-acids types, values : 0 or [] + dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions (dicts of dicts) : + actually, the three first dictionaries nested as values of keys codons/amico-acids/amico-acids + """ + + # I could have make sub-routines here. + # the copy commands are mandatory, otherwise all dictionaries will reference the same variable(s) + + dico_codons = {} + for codon in list_codons: + dico_codons[codon] = copy.deepcopy(content) + + dico_aa = {} + for aa in dict_genetic_code.keys(): + dico_aa[aa] = copy.deepcopy(content) + + dico_aatypes = {} + for aatype in dict_aa_classif.keys(): + dico_aatypes[aatype] = copy.deepcopy(content) + + dico_codons_transitions=copy.deepcopy(dico_codons) + for key in dico_codons_transitions.keys(): + dico_codons_transitions[key]=copy.deepcopy(dico_codons) + + dico_aa_transitions = copy.deepcopy(dico_aa) + for key in dico_aa_transitions.keys(): + dico_aa_transitions[key]=copy.deepcopy(dico_aa) + + dico_aatypes_transitions = copy.deepcopy(dico_aatypes) + for key in dico_aatypes_transitions.keys(): + dico_aatypes_transitions[key]=copy.deepcopy(dico_aatypes) + + return dico_codons, dico_aa, dico_aatypes, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions + +def viable(seqs, pos, method): + """ Compute if, among a set of sequences, either at least one of the codons at the specified position has not a "-", + or not any codon has a "-" + + Args : + seqs : a list (the sequences, which must all have the same size) + pos : an integer (the positions, <= len(seqs) -3) + + Returns: + bool + """ + codons = [seq[pos:pos+3] for seq in seqs] + if method == "all": + return not all("-" in codon for codon in codons) + elif method == "any": + return not any("-" in codon for codon in codons) + +# # # Function for codons, aa, aatypes Countings ------------------------------------------------------------------------------- + +def computeAllCountingsAndFreqs(seq, list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif): + """ Call all functions dedicated to the computation of occurences and frequencies of codons, amino-acids, amino-acids types + + Args : see sub-routines + + Returns : 6 dictionaries (occurences and frequencies for codons, amino-acids, amino-acids types). See sub-routines for details. + """ + + # ------ Sub-routines ------ # + + def codonsCountings(seq, list_codons, init_dict_codons): + """ Count occurences of each codon in a sequence + First reading frame only : input sequence is supposed to be an ORF + + Args : + seq (str) : the sequence + list_codons (list of str) : all codons except codons-stop + init_dict_codons (dict) : {codon1 : 0, codon2: 0, ...} + + Return : + codon (dict) : codons (keys) and their occurences (values) in the sequence + """ + + codons = copy.deepcopy(init_dict_codons) + + l = len(seq) + + if l%3 == 0: max_indice = l-3 + if l%3 == 1: max_indice = l-4 + if l%3 == 2: max_indice = l-5 + + for codon in range(0,max_indice+1,3): + if "-" not in seq[codon:codon+3] : + codons[seq[codon:codon+3]] += 1 + + return codons + + def codonsFreqs(dict_codons_counts): + """ Computes frequencies of each codon in a sequence + + Args : + dict_codons (dict) : the output of codonsCounting() + + Return : + codons_freqs (dict) : codons (keys) and their frequencies (values) + """ + + codons_freqs = {} + + for key in dict_codons_counts.keys(): + freq = float(dict_codons_counts[key])/sum(dict_codons_counts.values()) + codons_freqs[key] = freq + + return codons_freqs + + def aaCountings(dict_codons, dict_genetic_code, init_dict_aa): + """ Count occurences of each amino-acid in a sequence, based on the countings of codons (1st ORF) + + Args : + dict_codons (dict) : the output of codonsCounting() + dict_genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...} + init_dict_aa (dict) : {aa1 : 0, aa2: 0, ...} + + Return : + dict_aa (dict) : amino-acids (keys) and their occurences (values) + """ + dict_aa = copy.deepcopy(init_dict_aa) + + for key in dict_codons.keys(): + for value in dict_genetic_code.values(): + if key in value: + dict_aa[dict_genetic_code.keys()[dict_genetic_code.values().index(value)]] += dict_codons[key] + + return dict_aa + + def aaFreqs(dict_aa_counts): + """ Computes frequencies of each amino-acid in a sequence, based on the countings of codons (1st ORF) + + Args : + dict_aa_counts (dict) : the output of aaCountings() + + Return : + dict_aa_freqs (dict) : amino-acids (keys) and their frequencies (values) + """ + + dict_aa_freqs = {} + + for key in dict_aa_counts.keys(): + freq = float(dict_aa_counts[key])/sum(dict_aa_counts.values()) + dict_aa_freqs[key] = freq + + return dict_aa_freqs + + def aatypesCountings(dict_aa, dict_aa_classif, init_dict_classif): + """ Computes frequencies of each amino-acid type in a sequence, based on the countings of amino-acids (1st ORF) + + Args : + - dict_aa (dict) : the output of aaCountings() + - dict_aa_classif (dict) : the types of the amino-acids ( {type: [aa1, aa2, ...], ...} ) + - init_dict_classif (dict) : {'polar': 0, 'apolar': 0, ...} + + Return : + dict_aatypes (dict) : amino-acids types (keys) and their occurences (values) + """ + dict_aatypes = copy.deepcopy(init_dict_classif) + + for key_classif in dict_aa_classif.keys(): + for key_aa in dict_aa.keys(): + if key_aa in dict_aa_classif[key_classif]: + dict_aatypes[key_classif] += dict_aa[key_aa] + + return dict_aatypes + + def aatypesFreqs(dict_aatypes): + """ Computes frequencies of each amino-acid type in a sequence, based on the countings of amino-acids (1st ORF) + + Args : + dict_aatypes (dict) : the output of aatypesCountings() + + Return : + dict_aatypes_freqs : amino-acids types (keys) and their frequencies (values) + """ + dict_aatypes_freqs = {} + + for key in dict_aatypes.keys(): + freq = float(dict_aatypes[key])/sum(dict_aatypes.values()) + dict_aatypes_freqs[key] = freq + + return dict_aatypes_freqs + + # ------ The function ------ # + + codons_c = codonsCountings(seq, list_codons, init_dict_codons) + codons_f = codonsFreqs(codons_c) + aa_c = aaCountings(codons_c, dict_genetic_code, init_dict_aa) + aa_f = aaFreqs(aa_c) + aat_c = aatypesCountings(aa_c, dict_aa_classif, init_dict_classif) + aat_f = aatypesFreqs(aat_c) + + return codons_c, codons_f, aa_c, aa_f, aat_c, aat_f + +# # # Functions for various measures (ivywrel, ekqh...) ------------------------------------------------------------------------- + +def computeVarious(seq, dict_aa_counts, dict_aa_types): + """ Call al the functions for nucleic and amino-acids sequences description + + Args : See sub-routines for details. + + Returns : 6 integer or floats. See sub-routines for details. + """ + + # ------ Sub-routines ------ # + + def nbCodons(seq): + """ Compute the number of full codons in a sequence + Arg : seq (str): the sequence + Return: nb_codons (int) + """ + l = len(seq) + if l%3 == 0: nb_codons = l/3 + if l%3 == 1: nb_codons = (l-1)/3 + if l%3 == 2: nb_codons = (l-2)/3 + return nb_codons + + def maxIndice(seq): + """ Compute the highest indice for parsing a sequence + Arg : seq (str): the sequence + Return : max_indice (int) + """ + l = len(seq) + if l%3 == 0: max_indice = l-3 + if l%3 == 1: max_indice = l-4 + if l%3 == 2: max_indice = l-5 + return max_indice + + def gc12Andgc3Count(seq, nb_codons, max_indice): + """ Compute the frequency of gc12 in a sequence + Arg : seq (str) : the sequence + Return : (float) + """ + + # TO IMPROVE ? : make this computation in the codonCountigns() function to avoid parsing twice the sequence ? + # But : involves a less readable code + + gc12 = 0 + gc3 = 0 + + for i in range(0, max_indice+1,3): + if seq[i] in ["c","g"]: gc12 += 1 + if seq[i+1] in ["c","g"]: gc12 += 1 + if seq[i+2] in ["c","g"] or seq[i+2] in ["c","g"]: gc3 += 1 + + return float(gc3)/nb_codons, float(gc12)/(2*nb_codons) + + def ivywrelCount(nb_codons, dict_aa_counts): + """ Compute the sum of occurences of amino-acids IVYWREL divided by the number of codons + + Args : + nb_codons (int) : the number of codons in the sequence + dict_aa_counts (dict) : the output of aaCountings() + + return : (float) + """ + + IVYWREL = 0 + + for aa in ["I","V","Y","W","R","E","L"]: # Impossible to make a simple sum, in case one the aa is not in the dict keys + if aa in dict_aa_counts.keys(): + IVYWREL += dict_aa_counts[aa] + + return float(IVYWREL)/nb_codons + + def ekqhCount(dict_aa_counts): + """ Compute the ratio of amino-acids EK/QH + Arg : dict_aa_counts (dict) : the output of aaCountings() + Return : (float) + """ + ek = 0 + qh = 0 + + ek = dict_aa_counts["E"] + dict_aa_counts["K"] + qh = dict_aa_counts["Q"] + dict_aa_counts["H"] + + if qh != 0: + return float(ek)/qh + else : return ek + + def payresdgmCount(dict_aa_counts): + """ Compute the ratio of amino-acids PASRE/SDGM + Arg : dict_aa_counts (dict) : the output of aaCountings() + Return : (float) + """ + payre = 0 + sdgm = 0 + + for aa in ["P","A","Y","R","E"]: + payre += dict_aa_counts[aa] + for aa in ["S","D","G","M"]: + sdgm += dict_aa_counts[aa] + + if sdgm != 0: + return float(payre)/sdgm + else : return payre + + def purineLoad(seq, nb_codons): + """ Compute the purine load indice of a sequence + Args : + seq (str) : the sequence + nb_codons (int) : the number of codons in the sequence + + Return (float) + """ + + # TO IMPROVE ? : make this computation in the codonCountigns() function to avoid parsing twice the sequence ? + # But : involves a less readable code + + g12, g3, A, c12, c3, T = 0.0,0.0,seq.count("a"),0.0,0.0,seq.count("t") + + # g3 and c3 : g and c in 3rd position of a codon + s = "" + for i in range(2, len(seq), 3): + s += seq[i] + g3 = s.count("g") + c3 = s.count("c") + + # g12 and c12 : g and c in 1st and 2d positions of a codon + s = "" + for i in range(0, len(seq), 3): + s += seq[i] + g12 = s.count("g") + c12 = s.count("c") + s = "" + for i in range(1, len(seq), 3): + s += seq[i] + g12 += s.count("g") + c12 += s.count("c") + + return float(1000*(g12+g3+A-c12-c3-T))/(3*nb_codons) + + def cvp(dict_aatypes): + """ Compute the difference nb_charged_aamino_acids - nb_polar_amino_acids + Return: (int) + """ + return dict_aatypes["charged"] - dict_aatypes["polar"] + + # ------ The function ------ # + + nb_codons = nbCodons(seq) + max_indice = maxIndice(seq) + GC3, GC12 = gc12Andgc3Count(seq, nb_codons, max_indice) + IVYWREL, EKQH, PAYRESDGM = ivywrelCount(nb_codons, dict_aa_counts), ekqhCount(dict_aa_counts), payresdgmCount(dict_aa_counts) + purineload, CvP = purineLoad(seq, nb_codons), cvp(dict_aa_types) + return GC3, GC12, IVYWREL, EKQH, PAYRESDGM, purineload, CvP + +# # # Function for codons, aa, aatypes Transitions ----------------------------------------------------------------------------- + +def computeAllBiases(seq1, seq2, dico_codons_transi, dico_aa_transi, dico_aatypes_transi, reversecode, reverseclassif) : + """ Compute all biases (transisitions codon->codon, aa->-aa, aa_type->aa_type) between two sequences + + Args : See sub-routines for details + + Returns 3 dictionaries of dictionaries. See sub-routines for details + """ + + # ------ Sub-routines ------ # + + def codons_transitions(seq1, seq2, dico_codons_transi): + """ Compute the number of transitions from a codon of a sequence to the codon of a second sequence + + Args : + seq1 (str) : the first sequence + seq2 (str) : the second sequence + dico_codons_transi (dict of dicts) : { codon1 : {codon1: 0, codon2 : 0, ...}, ..} + + Return : + codons_transi (dict of dicts) : the occurences of each codon to codon transition + """ + + codons_transi = copy.deepcopy(dico_codons_transi) + + for i in range(0, len(seq1), 3): + # check if no indel and if len seq[i:i+3] is really 3 (check for the last codon) + if viable([seq1, seq2], i, "any") and len(seq1[i:i+3]) == 3 and len(seq2[i:i+3]) == 3 : + codons_transi[seq1[i:i+3]][seq2[i:i+3]] += 1 + + return codons_transi + + def codons_transitions_freqs(codons_transitions_counts): + """ Computes frequencies of codon transitions between two sequences + + Arg : + codons_transitions_counts (dict) : the output of codons_transitions() + + Return : + codons_transi_freqs (dict of dicts) : the frequencies of each codon to codon transition + """ + + codons_transi_freqs = {} + + for key in codons_transitions_counts.keys(): + codons_transi_freqs[key] = {} + for key2 in codons_transitions_counts[key].keys(): + if sum(codons_transitions_counts[key].values()) != 0: + freq = float(codons_transitions_counts[key][key2])/sum(codons_transitions_counts[key].values()) + codons_transi_freqs[key][key2] = freq + else : + codons_transi_freqs[key][key2] = 0 + return codons_transi_freqs + + def aa_transitions(dico_codons_transi, dico_aa_transi, reversecode): + """ Compute the number of transitions from an amino-acid of a sequence to the amino-acid of a second sequence + + Args : + dico_codons_transi (dict of dicts) : the codons transitions computed by codons_transitions() + dico_aa_transi (dict of dicts) : { aa1 : {aa1: 0, aa2 : 0, ...}, ..} + reversecode (dict) : the reversed genetic code {aa1 : [codons],...} -> {codon1: aa1, codon2: aa2, ...} + + Return : + aa_transi (dict of dicts) : the occurences of each aa to aa transition + """ + + aa_transi = copy.deepcopy(dico_aa_transi) + + for k in dico_codons_transi.keys(): + newk = reversecode[k] + for k2 in dico_codons_transi[k].keys(): + newk2 = reversecode[k2] + aa_transi[newk][newk2] += dico_codons_transi[k][k2] + + return aa_transi + + def aa_transitions_freqs(aa_transitions_counts): + """ Computes frequencies of amico-acids transitions between two sequences + Arg : aa_transitions_counts (dict of dicts): the output of aa_transitions() + Return : aa_transi_freqs (dict of dicts) : the frequencies of each aa to aa transition + """ + + aa_transi_freqs = {} + + for key in aa_transitions_counts.keys(): + aa_transi_freqs[key] = {} + for key2 in aa_transitions_counts[key].keys(): + if sum(aa_transitions_counts[key].values()) != 0: + freq = float(aa_transitions_counts[key][key2])/sum(aa_transitions_counts[key].values()) + aa_transi_freqs[key][key2] = freq + else : + aa_transi_freqs[key][key2] = 0 + return aa_transi_freqs + + def aatypes_transitions(dico_aa_transi, dico_aatypes_transi, reverseclassif): + """ Compute the number of transitions from an amino-acid type of a sequence to the amino-acid type of a second sequence + + Args : + dico_aa_transi (dict of dicts) : the output of aa_transitions() + dico_aatypes_transi (dict of dicts) : { type1 : {type1: 0, type2 : 0, ...}, ..} + reverseclassif (dict) : the reversed amino-acid clasification {aa1: type, aa2: type, ...} + + Return : + aatypes_transi (dict of dicts) : the occurences of each aatype to aatype transition + """ + + aatypes_transi = copy.deepcopy(dico_aatypes_transi) + for k in dico_aa_transi.keys(): + newk = reverseclassif[k] + for k2 in dico_aa_transi[k].keys(): + newk2 = reverseclassif[k2] + aatypes_transi[newk][newk2] += dico_aa_transi[k][k2] + + return aatypes_transi + + def aatypes_transitions_freqs(aatypes_transitions_counts): + """ Computes frequencies of amico-acids types transitions between two sequences + Args : aatypes_transitions_counts (dict of dicts) : the output of aatypes_transitions() + Return : aatypes_transi_freqs (dict of dicts) : the frequencies of each aatype to aatype transition + """ + + aatypes_transi_freqs = {} + + for key in aatypes_transitions_counts.keys(): + aatypes_transi_freqs[key] = {} + for key2 in aatypes_transitions_counts[key].keys(): + if sum(aatypes_transitions_counts[key].values()) != 0: + freq = float(aatypes_transitions_counts[key][key2])/sum(aatypes_transitions_counts[key].values()) + aatypes_transi_freqs[key][key2] = freq + else : + aatypes_transi_freqs[key][key2] = 0 + return aatypes_transi_freqs + + + + + # ------ The function ------ # + + codons_transitions = codons_transitions(seq1, seq2, dico_codons_transi) + codons_transitions_freqs = codons_transitions_freqs(codons_transitions) + aa_transitions = aa_transitions(codons_transitions, dico_aa_transi, reversecode) + aa_transitions_freqs = aa_transitions_freqs(aa_transitions) + aatypes_transitions = aatypes_transitions(aa_transitions, dico_aatypes_transi, reverseclassif) + aatypes_transitions_freqs = aatypes_transitions_freqs(aatypes_transitions) + + return codons_transitions, codons_transitions_freqs, aa_transitions, aa_transitions_freqs, aatypes_transitions, aatypes_transitions_freqs + +def all_sed(codons_c, aa_c, aat_c, codons_transitions, aa_transitions, aatypes_transitions, dico_codons_transi, dico_aa_transi, dico_aatypes_transi): + + def compute_sed(transi, counts, dico): + """ Compute the substitution exchangeability disequilibrium (SED) from one species A to another B between codons/aa//aatypes couples + + Args: + transi ; dict - dictionaries of all counts of transition from codon/aa/aatype X to Y from sp A to sp B + counts : dict - dictionaries of codons/aa/aatypes counts in species A + dico : dict - a dictionary (nested) with all values to 0 + + """ + dict_sed = copy.deepcopy(dico) + + for key in transi.keys(): + for key2 in transi.keys(): + if counts[key] != 0 and float(transi[key2][key])/counts[key] != 0.0: + x = (float(transi[key][key2])/counts[key]) / (float(transi[key2][key])/counts[key]) + dict_sed[key][key2] = - pow(2,1-x)+1 + else : + dict_sed[key][key2] = 'NA' + + return dict_sed + + codons_sed = compute_sed(codons_transitions, codons_c, dico_codons_transi) + aa_sed = compute_sed(aa_transitions, aa_c, dico_aa_transi) + aatypes_sed = compute_sed(aatypes_transitions, aat_c, dico_aatypes_transi) + + return codons_sed, aa_sed, aatypes_sed + +# # # Function for random resampling -------------------------------------------------------------------------------------------- + +def sampling (dict_seq, nb_iter, len_sample, list_codons, genetic_code, aa_classif, reversecode, reverseclassif): + """ Resample randomly codons from sequences (sort of bootsrap) + + Args : + dict_seq (dict) : contains the species name and sequences used ( { 'sp1': seq1, 'sp2': seq2, ...}) without '-' removal + nb_iter (int) : number of resampling iterations (better >= 1000) + len_sample (int) : length (in codons) of a resampled sequence (better >= 1000) + list_codons (list of str): all codons except codons-stop + genetic_code (dict) : the genetic code : {'aa1': [codon1, codon2,...], ...} + aa_classif (dict) : the types of the amino-acids : {type: [aa1, aa2, ...], ...} + reversecode (dict) : the reversed genetic code : {codon1: aa1, codon2: aa2, ...} + reverseclassif (dict) : the reversed amino-acid : clasification {aa1: type, aa2: type, ...} + + Returns : + codons_lst, aa_lst, classif_lst (dicts) : keys : codons/aa/aatypes, values : [] + codons_transitions_lst, aa_transitions_lst, classif_transitions_lst (dict of dicts) : keys : codons/aa/aatypes, values : the 3 previous dicts + """ + + # Initialize empty dictionaries for countings and transitions. It's also possible to isntanciate these ones in the main() but it would make a function with ~14 parameters + codons_0, aa_0, classif_0, codons_transitions_0, aa_transitions_0, classif_transitions_0 = buildDicts(list_codons, 0, genetic_code, aa_classif) + codons_lst, aa_lst, classif_lst, codons_transitions_lst, aa_transitions_lst, classif_transitions_lst = buildDicts(list_codons, [], genetic_code, aa_classif) + + # determine the max position where sampling is possible + l = len(dict_seq.values()[1]) + if l%3 == 0: max_indice = l-3 + if l%3 == 1: max_indice = l-4 + if l%3 == 2: max_indice = l-5 + + # List of positions to resample + viable_positions = [pos for pos in range(0,max_indice,3) if viable(dict_seq.values(), pos, "all")] + sample_positions = np.random.choice(viable_positions, len_sample) + + # nb_iter resampled sequences + for i in range(nb_iter): + if (i+1)%(nb_iter/10) == 0: + print " "+str( (i+1)*100/nb_iter)+"%" + + seqa, seqb = "", "" + for pos in sample_positions: + codona, codonb = "---", "---" + # The sequence to be resampled in this position is randomly chosen ; no "-" resampled + while "-" in codona : + codona = dict_seq.values()[random.randrange(0, len(dict_seq.keys())-1)][pos:pos+3] + while "-" in codonb : + codonb = dict_seq.values()[random.randrange(0, len(dict_seq.keys())-1)][pos:pos+3] + seqa += codona + seqb += codonb + + # dictionaries : frequences of codons, aa, aatypes (seq1) + codons_occ_tmp, codons_freq_tmp, aa_occ_tmp, aa_freq_tmp, aatypes_occ_tmp, aatypes_freq_tmp = computeAllCountingsAndFreqs(seqa, list_codons, codons_0, aa_0, classif_0, genetic_code, aa_classif) + # dictionaries frequences of transitions (seqa->seqb) + codons_transitions_tmp, codons_transitions_freq_tmp, aa_transition_tmp, aa_transitions_freq_tmp, aatypes_transitions_tmp, aatypes_transitions_freq_tmp = computeAllBiases(seqa, seqb, codons_transitions_0, aa_transitions_0, classif_transitions_0, reversecode, reverseclassif) + + # Adding occurrences in final dicts + for key in codons_freq_tmp.keys(): + codons_lst[key].append(codons_freq_tmp[key]) + for key in aa_freq_tmp.keys(): + aa_lst[key].append(aa_freq_tmp[key]) + for key in aatypes_freq_tmp.keys(): + classif_lst[key].append(aatypes_freq_tmp[key]) + + # Adding occurrences in final dicts (transitions) + for key in codons_transitions_freq_tmp.keys(): + for key2 in codons_transitions_freq_tmp[key].keys(): + codons_transitions_lst[key][key2].append(codons_transitions_freq_tmp[key][key2]) + for key in aa_transitions_freq_tmp.keys(): + for key2 in aa_transitions_freq_tmp[key].keys(): + aa_transitions_lst[key][key2].append(aa_transitions_freq_tmp[key][key2]) + for key in aatypes_transitions_freq_tmp.keys(): + for key2 in aatypes_transitions_freq_tmp[key].keys(): + classif_transitions_lst[key][key2].append(aatypes_transitions_freq_tmp[key][key2]) + + return codons_lst, aa_lst, classif_lst, codons_transitions_lst, aa_transitions_lst, classif_transitions_lst + +def testPvalues(dict_counts, dict_resampling, nb_iter, method): + """ Computes where the observed value is located in the expected counting distribution + + Args : + dict_counts (dict) : observed frequencies obtained from the functions computeAllCountingsAndFreqs() or computeAllBiases() + dict_resampling (dict) : expected frequencies obtained from the functions computeAllCountingsAndFreqs() or computeAllBiases() within the sampling() function + + Return : + pvalue (dict, dict of dicts) : the pvalues of all observed countings (dict) and transitions (dict of dicts) + + + pnorm computes the pvalue to have a value inferior to the observed value under a normal distribution + One sided to left tail : + p < 0.05 indicates significantly lower counts + p > 0.95 indicates significantly higher counts + """ + + + def p_resampling(obs, values, nb_iter): + """ The pvalue is the proportion of bootsrapped values smaller than the observed value + If p = 0.025 : 2.5% of the bootstrapped values are smaller than the observed value + p < 0.025 : the obs value is most likely significantly lower. + If p = 0.975 : 97.5% of the bootstrapped values are smaller than the observed value + p > 0.975 the obs value is most likely significantly higher. + + Args : + obs : int or float - the observed value + values : list - values of resampling (int or floats) + nb_iter : int - the number of resampled values (=len(values)) + + Return : + pvalue (float) + """ + + num = len([x for x in values if x < obs]) + return float(num + 1) / (nb_iter+1) + + def testPvalue(obs, exp, nb_iter): + """ Compute a pvalue + + Args : + exp (list of floatsà : a list of length nb_iter, containing expected frequencies of a codon/aa/aatype at each iteration + obs (float) : the observed value + nb_iter (int) : the number of iterations for resampling + + Returns : + pvalue (float) + """ + + max_val = nb_iter-1 + min_val = 0 + test_val = (max_val+min_val)/2 + + while max_val-min_val > 1: + if obs > exp[test_val]: + min_val = test_val + test_val = (max_val+min_val)/2 + elif obs < exp[test_val]: + max_val = test_val + test_val = (max_val+min_val)/2 + else: + break + + pvalue = float(test_val+1)/(nb_iter+1) + + return pvalue + + # ------ The function ------ # + + pvalues = {} + + for key in dict_resampling.keys(): + if type(dict_resampling.values()[1]) is not dict : + if method == 'origin': + pvalues[key] = testPvalue(dict_counts[key], dict_resampling[key], nb_iter) + elif method == 'pnorm': + pvalues[key] = scipy.stats.norm.cdf(dict_counts[key], np.mean(dict_resampling[key]), np.std(dict_resampling[key])) + elif method == 'p_resampling': + pvalues[key] = p_resampling(dict_counts[key], dict_resampling[key], nb_iter) + else : + pvalues[key] = {} + for key2 in dict_resampling[key].keys(): + if method == 'origin': + pvalues[key][key2] = testPvalue(dict_counts[key][key2], dict_resampling[key][key2], nb_iter) + elif method == 'pnorm': + pvalues[key][key2] = scipy.stats.norm.cdf(dict_counts[key][key2], np.mean(dict_resampling[key][key2]), np.std(dict_resampling[key][key2])) + elif method == 'p_resampling': + pvalues[key][key2] = p_resampling(dict_counts[key][key2], dict_resampling[key][key2], nb_iter) + + return pvalues + +def main(): + + # arguments + parser = argparse.ArgumentParser() + parser.add_argument("sequences_file", help="File containing sequences (the output of the tool 'ConcatPhyl'") + parser.add_argument("considered_species", help="The species name, separated by commas (must be the same than in the sequences_file). It is possible to consider only a subset of species.") + parser.add_argument("species_for_bootstrap", help="The species which will be used for bootstrapping, separated by commas. It is possible to consider only a subset of species.") + parser.add_argument("iteration", help="The number of iterations for bootstrapping (better if => 1000)", type=int) + parser.add_argument("sample_length", help="The lenght of a bootstrapped sequences (better if >= 1000", type=int) + args = parser.parse_args() + + print "\n ------ Occurences and frequencies of codons, amino-acids, amino-acids types -------\n" + + print "The script counts the number of codons, amino acids, and types of amino acids in sequences," + print "as well as the mutation bias from one item to another between 2 sequences.\n" + + print "Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences." + print "In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from" + print "a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting." + + print " Sequences file : {}".format(args.sequences_file) + print " Species retained for countings : {}\n".format(args.considered_species) + + print "Processing : reading input file, opening output files, building dictionaries." + + # make pairs + list_species = str.split(args.considered_species, ",") + list_species_boot = str.split(args.species_for_bootstrap, ",") + pairs_list=list(itertools.combinations(list_species,2)) + + # read sequences + sequences_for_counts = {} + sequences_for_resampling = {} + with open(args.sequences_file, "r") as file: + for line1,line2 in itertools.izip_longest(*[file]*2): + species = line1.strip(">\r\n") + sequence = line2.strip("\r\n") + if species in list_species: + sequences_for_counts[species] = sequence + if species in list_species_boot: + sequences_for_resampling[species] = sequence + + print " Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences." + print " Frequences are more representative." + + print "\n Indels percent :" + + for k,v in sequences_for_counts.items(): + print " {} : {} %".format(k, float(v.count("-"))/len(v)*100) + + # useful dictionaries + dict_genetic_code={"F":["ttt","ttc"], + "L":["tta","ttg","ctt","ctc","cta","ctg"], + "I":["att","atc","ata"], + "M":["atg"], + "V":["gtt","gtc","gta","gtg"], + "S":["tct","tcc","tca","tcg","agt","agc"], + "P":["cct","cca","ccg","ccc"], + "T":["act","acc","aca","acg"], + "A":["gct","gcc","gca","gcg"], + "Y":["tat","tac"], + "H":["cat","cac"], + "Q":["caa","cag"], + "N":["aat","aac"], + "K":["aaa","aag"], + "D":["gat","gac"], + "E":["gaa","gag"], + "C":["tgt","tgc"], + "W":["tgg"], + "R":["cgt","cgc","cga","cgg","aga","agg"], + "G":["ggt","ggc","gga","ggg"]} + + dict_aa_classif={"unpolar":["G","A","V","L","M","I"], + "polar":["S","T","C","P","N","Q"], + "charged":["K","R","H","D","E"], + "aromatics":["F","Y","W"]} + + reversecode={v:k for k in dict_genetic_code for v in dict_genetic_code[k]} + reverseclassif={v:k for k in dict_aa_classif for v in dict_aa_classif[k]} + + # codons list (without stop codons) + nucleotides = ['a', 'c', 'g', 't'] + list_codons = [''.join(comb) for comb in itertools.product(nucleotides, repeat=3)] + list_codons.remove("taa") + list_codons.remove("tag") + list_codons.remove("tga") + + # Store already computed species + row.names in output files + index = [] + index_transi = [] + + # Final dictionaries writed to csv files + all_codons = {} + all_aa = {} + all_aatypes = {} + all_various = {} + all_codons_transitions = {} # Not used because too much : 61*61 columns + all_aa_transitions = {} + all_aatypes_transitions = {} + + # RUN + + print "\nProcessing : resampling ..." + print " Parameters : {niter} iterations, {lensample} codon per resampled sequence, species used : {species}\n".format(niter=args.iteration, lensample=args.sample_length, species=args.species_for_bootstrap) + + codons_boot, aa_boot, aatypes_boot, codons_transi_boot, aa_transi_boot, aatypes_transi_boot = sampling(sequences_for_resampling, args.iteration, args.sample_length, list_codons, dict_genetic_code, dict_aa_classif, reversecode, reverseclassif) + print " Done.\n" + + print "Processing : countings....\n" + + # Initialize empty dictionaries for countings and transitions + init_dict_codons, init_dict_aa, init_dict_classif, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions = buildDicts(list_codons, 0, dict_genetic_code, dict_aa_classif) + + for pair in pairs_list: + p1, p2 = pair[0], pair[1] + if p1 not in index: + print "Countings on {}".format(p1) + + p1_codons_counts, p1_codons_freqs, p1_aa_counts, p1_aa_freqs, p1_aatypes_counts, p1_aatypes_freqs = computeAllCountingsAndFreqs(sequences_for_counts[p1], list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif) + p1_GC3, p1_GC12, p1_IVYWREL, p1_EKQH, p1_PAYRESDGM, p1_purineload, p1_CvP = computeVarious(sequences_for_counts[p1], p1_aa_counts, p1_aatypes_freqs) + + + p1_codons_pvalues = testPvalues(p1_codons_freqs, codons_boot, args.iteration, 'p_resampling') + p1_aa_pvalues = testPvalues(p1_aa_freqs, aa_boot, args.iteration, 'p_resampling') + p1_aatypes_pvalues = testPvalues(p1_aatypes_freqs, aatypes_boot, args.iteration, 'p_resampling') + + all_codons[p1+"_obs_counts"] = p1_codons_counts + all_codons[p1+"_obs_freqs"] = p1_codons_freqs + all_codons[p1+"_pvalues"] = p1_codons_pvalues + all_aa[p1+"_obs_counts"] = p1_aa_counts + all_aa[p1+"_obs_freqs"] = p1_aa_freqs + all_aa[p1+"_pvalues"] = p1_aa_pvalues + all_aatypes[p1+"_obs_counts"] = p1_aatypes_counts + all_aatypes[p1+"_obs_freqs"] = p1_aatypes_freqs + all_aatypes[p1+"_pvalues"] = p1_aatypes_pvalues + all_various[p1] = [p1_GC3, p1_GC12, p1_IVYWREL, p1_EKQH, p1_PAYRESDGM, p1_purineload, p1_CvP] + + index.append(p1) + + if p2 not in index: + print "Countings on {}".format(p2) + + p2_codons_counts, p2_codons_freqs, p2_aa_counts, p2_aa_freqs, p2_aatypes_counts, p2_aatypes_freqs = computeAllCountingsAndFreqs(sequences_for_counts[p2], list_codons, init_dict_codons, init_dict_aa, init_dict_classif, dict_genetic_code, dict_aa_classif) + p2_GC3, p2_GC12, p2_IVYWREL, p2_EKQH, p2_PAYRESDGM, p2_purineload, p2_CvP = computeVarious(sequences_for_counts[p2], p2_aa_counts, p2_aatypes_freqs) + + p2_codons_pvalues = testPvalues(p2_codons_freqs, codons_boot, args.iteration, 'p_resampling') + p2_aa_pvalues = testPvalues(p2_aa_freqs, aa_boot, args.iteration, 'p_resampling') + p2_aatypes_pvalues = testPvalues(p2_aatypes_freqs, aatypes_boot, args.iteration, 'p_resampling') + + all_codons[p2+"_obs_counts"] = p2_codons_counts + all_codons[p2+"_obs_freqs"] = p2_codons_freqs + all_codons[p2+"_pvalues"] = p2_codons_pvalues + all_aa[p2+"_obs_counts"] = p2_aa_counts + all_aa[p2+"_obs_freqs"] = p2_aa_freqs + all_aa[p2+"_pvalues"] = p2_aa_pvalues + all_aatypes[p2+"_obs_counts"] = p2_aatypes_counts + all_aatypes[p2+"_obs_freqs"] = p2_aatypes_freqs + all_aatypes[p2+"_pvalues"] = p2_aatypes_pvalues + all_various[p2] = p2_GC3, p2_GC12, p2_IVYWREL, p2_EKQH, p2_PAYRESDGM, p2_purineload, p2_CvP + + index.append(p2) + + if (p1, p2) not in index_transi and p1 in sequences_for_counts and p2 in sequences_for_counts: + print "Countings transitions between {} and {}".format(p1, p2) + codons_transitions, codons_transitions_freqs, aa_transitions, aa_transitions_freqs, aatypes_transitions, aatypes_transitions_freqs = computeAllBiases(sequences_for_counts[p1], sequences_for_counts[p2], dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions, reversecode, reverseclassif) + + # Ajout + codons_sed, aa_sed, aatypes_sed = all_sed(p1_codons_counts, p1_aa_counts, p1_aatypes_counts, codons_transitions, aa_transitions, aatypes_transitions, dico_codons_transitions, dico_aa_transitions, dico_aatypes_transitions) + + index_transi.append((p1,p2)) + + p1p2_codons_pvalues = testPvalues(codons_transitions_freqs, codons_transi_boot, args.iteration, 'p_resampling') + p1p2_aa_pvalues = testPvalues(aa_transitions_freqs, aa_transi_boot, args.iteration, 'p_resampling') + p1p2_aatypes_pvalues = testPvalues(aatypes_transitions_freqs, aatypes_transi_boot, args.iteration, 'p_resampling') + + all_codons_transitions[p1+">"+p2+"_obs_counts"] = codons_transitions + all_codons_transitions[p1+">"+p2+"_obs_freqs"] = codons_transitions_freqs + all_codons_transitions[p1+">"+p2+"_pvalues"] = p1p2_codons_pvalues + all_aa_transitions[p1+">"+p2+"_obs_counts"] = aa_transitions + all_aa_transitions[p1+">"+p2+"_obs_freqs"] = aa_transitions_freqs + all_aa_transitions[p1+">"+p2+"_pvalues"] = p1p2_aa_pvalues + all_aatypes_transitions[p1+">"+p2+"_obs_counts"] = aatypes_transitions + all_aatypes_transitions[p1+">"+p2+"_obs_freqs"] = aatypes_transitions_freqs + all_aatypes_transitions[p1+">"+p2+"_pvalues"] = p1p2_aatypes_pvalues + + all_codons_transitions[p1+">"+p2+"_sed"] = codons_sed + all_aa_transitions[p1+">"+p2+"_sed"] = aa_sed + all_aatypes_transitions[p1+">"+p2+"_sed"] = aatypes_sed + + index_transi.append((p1, p2)) + + print "\n Done.\n" + + print "Processing : creating dataframes ..." + + frame_codons = pd.DataFrame(all_codons).T.astype('object') + frame_aa = pd.DataFrame(all_aa).T.astype('object') + frame_aatypes = pd.DataFrame(all_aatypes).T.astype('object') + + frame_codons_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_codons_transitions.items()}).unstack() + frame_codons_transitions.columns = frame_codons_transitions.columns.map('>'.join) + + frame_aa_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_aa_transitions.items()}).unstack() + frame_aa_transitions.columns = frame_aa_transitions.columns.map('>'.join) + + frame_aatypes_transitions = pd.concat({k: pd.DataFrame(v) for k, v in all_aatypes_transitions.items()}).unstack() + frame_aatypes_transitions.columns = frame_aatypes_transitions.columns.map('>'.join) + + frame_various = pd.DataFrame(all_various).T + frame_various.columns = ["GC3","GC12","IVYWREL","EKQH","PAYRESDGM","purineload", "CvP"] + + frame_codons.index.name, frame_aa.index.name, frame_aatypes.index.name = "Species", "Species","Species" + frame_aa_transitions.index.name, frame_aatypes_transitions.index.name, frame_various.index.name = "Species","Species","Species" + + print "Writing dataframes to output files ...\n" + + frame_codons.round(8).to_csv("codons_freqs.csv", sep=",", encoding="utf-8") + frame_aa.round(8).to_csv("aa_freqs.csv", sep=",", encoding="utf-8") + frame_aatypes.astype('object').round(8).to_csv("aatypes_freqs.csv", sep=",", encoding="utf-8") + frame_codons_transitions.round(8).to_csv("codons_transitions_freqs.csv", sep=",", encoding="utf-8") + frame_aa_transitions.round(8).to_csv("aa_transitions_freqs.csv", sep=",", encoding="utf-8") + frame_aatypes_transitions.round(8).to_csv("aatypes_transitions_freqs.csv", sep=",", encoding="utf-8") + frame_various.round(8).to_csv("gc_and_others_freqs.csv", sep=",", encoding="utf-8") + + print "Done." + +if __name__ == "__main__": + main() \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01b_extract_variable_nuc.py Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,121 @@ +#!/usr/bin/env python +#coding: utf-8 + +import argparse, os +from functions import dico, write_output, fill_with_NaN + +""" Functions for nucleic format """ + +def all_nuc_counts(seq): + """ Counts the number of nucleotides in a sequence + + Args : + - seq (String) : a nucleic sequence + + Return: + - nuc_counts (dict) : counts on nucleotides (key/value : nucleotide/count) + """ + nuc_counts = {} + seqU = seq.upper() + LN =['A','C','T','G'] + + for base in LN: + nuc_counts[base] = seqU.count(base) + + return nuc_counts + +def ratios(nuc_counts): + """ Compute GC and purine ratios from the counts of nucleotides in a sequence + + Args : + - nuc_counts (dict) : dictionary of nucleotides counts (output of all_nuc_counts()) + + Return : + - ratios (dict) : dictionary with ratios + """ + + # Search for compositional bias in genome as marker of thermal adaptation + ratios = {} + ratios['GC_percent'] = float(nuc_counts['C'] + nuc_counts['G'])/(sum(nuc_counts.values())*100) + ratios['purine_percent'] = float(nuc_counts['A'] + nuc_counts['G'])/(sum(nuc_counts.values())*100) + + ratios['DIFF_GC'] = nuc_counts['G'] - nuc_counts['C'] + ratios['DIFF_AT'] = nuc_counts['A'] - nuc_counts['T'] + + # Per bp + ratios['PLI_GC'] = float(ratios['DIFF_GC'])/sum(nuc_counts.values()) + ratios['PLI_AT'] = float(ratios['DIFF_AT'])/sum(nuc_counts.values()) + + # Per 1000 bp + ratios['PLI_GC_1000'] = ratios['PLI_GC']*1000 + ratios['PLI_AT_1000'] = ratios['PLI_AT']*1000 + + return ratios + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("species_list", help="List of species separated by commas") + args = parser.parse_args() + + LN =['A','C','T','G'] + Lratios = ['GC_percent', 'purine_percent', 'DIFF_GC', 'DIFF_AT', 'PLI_GC', 'PLI_AT', 'PLI_GC_1000', 'PLI_AT_1000'] + + list_inputs = [] + + path_inputs = '01_input_files' + list_inputs = os.listdir(path_inputs) + + lsp = args.species_list.split(',') + lsp = sorted(lsp) + flsp = '' + for el in lsp: + flsp += el+',' + + path_outputs_1 = '02_tables_per_nucleotide' + path_outputs_2 = '02_tables_per_nuc_variable' + os.mkdir(path_outputs_1) + os.mkdir(path_outputs_2) + + dict_for_files_nuc = {} + dict_for_file_var = {} + + # All counts + for file in list_inputs: + # iterate over input files + sequences = dico(file, path_inputs) + + # TEMPORARY CORRECTION FOR SEQUENCES CONTAINING ONLY INDELS + # It appears than CDS_Search can bug sometimes and return an alignement where a species' sequence is made of indels only + # This causes a crash here (in the ratios function). The correction skip the whole file. + # When CDS_Search is corrected, lines with 'skip' can be removed + skip = False + for key in sequences.keys(): + if all(x == '-' for x in sequences[key]): + skip = True + + if not skip: + + nuc_counts_per_seq = {} + nuc_var_per_seq = {} + + for key in sequences.keys(): + # iterate over sequences in the file + nuc_counts_per_seq[key] = all_nuc_counts(sequences[key]) + nuc_var_per_seq[key] = ratios(nuc_counts_per_seq[key]) + + # Add NaN for missing species + for key in set(lsp).difference(set(sequences.keys())): + nuc_counts_per_seq[key] = fill_with_NaN(LN) + nuc_var_per_seq[key] = fill_with_NaN(Lratios) + + # Add computations to final dicts + dict_for_files_nuc[file] = nuc_counts_per_seq + dict_for_file_var[file] = nuc_var_per_seq + + + # Try with pandas ? + write_output(LN, flsp, path_outputs_1, dict_for_files_nuc) # one file per nuc + write_output(Lratios, flsp, path_outputs_2, dict_for_file_var) # one file per nuc_variable + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01b_extract_variable_prot.py Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,321 @@ +#!/usr/bin/env python +#coding: utf-8 +#Author : Eric Fontanillas (2010) - Victor Mataigne (2018) + +# TODO : + # - Deal with missing data : do not do the sign test if missing species in a group + # - Find a way to avoid the list_species argument + +import argparse, os +from functions import dico, write_output, fill_with_NaN + +def aa_properties(amino_acids_properties_file): + """ Read the file 'amino_acids_properties' and stores its content + + Args : + amino_acids_properties_file (String) : the file + + Return : + aa_properties (dict) : key/amino-acid - value/list of properties + """ + + dict_aa_properties={} + with open(amino_acids_properties_file, 'r') as f: + f.readline() #jump headers + for line in f.readlines(): + S1 = line.split(",") + aa_name = S1[1] + S2 = aa_name.split("/") + aa_code = S2[1][:-1] + + frequencies = S1[2][:-1] + residue_weight = S1[5] + residue_volume = S1[6] + partial_specific_volume = S1[7] + hydration = S1[8] + + dict_aa_properties[aa_code] = [frequencies, residue_weight, residue_volume, partial_specific_volume, hydration] + + return(dict_aa_properties) + +""" Functions for proteic format """ + +def all_aa_counts(seq): + """ Count the occurrences of all amino-acids in a sequence + + Args: + seq (String) : a proteic sequence + + Returns: a dictionary with amino-acids counts + """ + + aa_counts = {} + seqU = seq.upper() + LAA =['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G'] + + for aa in LAA: + aa_counts[aa] = seqU.count(aa) + + return aa_counts + +def all_aa_props(seq_counts): + """ Converts a dictionnary of counts into a dictionnary of proportions + + Args: + seq_counts (dict) : dictionnary computed by the function all_aa_counts() + + Returns: a dictionary with counts replaced by proportions + """ + + aa_props = {} + for key in seq_counts.keys(): + aa_props[key] = float(seq_counts[key]) / sum(seq_counts.values()) + return aa_props + +def aa_variables_counts_and_props(aa_counts): + """ Computes several thermostability indices (summed occurrences of some AAs, and then various ratios) + + Args: + aa_counts (dict) : dictionnary computed by the function all_aa_counts() + + Returns: + aa_variables_counts : a dictionary with indices values + aa_variables_props : a dictionary with indices proportions (ratios excluded) + """ + + # Hyperthermophile Prokaryotes criterias + # IVYWREL : positivelly correlated with otpimal growth + # ERK : (i.e. ) => positivelly correlated with optimal growth temperature + # ERK/DNQTSHA (or DNQTSH ??) + # EK/QH + + # Mutationnal bias hypothesis => AT rich: favor FYMINK // GC rich: favor GARP + # The mutational bias model predict a linear relationship between GARP vs FYMINK + # ==> so if outliers to that, it means that the excess of GARP or FYMINK are not explained by the mutationnal bias model but by something else (selection ?) + + + # Hydophobicity hypothesis [should INCREASE with thermal adaptation] + # AL + # Only non-aromatic : AVLIM + # Only aromatic : FYW + + # Charged hypothesis => positivelly correlated with optimal growth temperature + # All charged : RHKDE + # Only positive : RHK + # Only negative : DE + + # Neutral polar hypothesis [should DECREASE with thermal adaptation] + # STNQ + + # Fontanillas' criteria + # PAYRE + # MVGDS + # PAYRE/MVGDS + + # Jollivet's criteria + # AC + # MVGDS + # AC/MVGDS + + aa_variables_counts = {} + aa_variables_props = {} + len_seq = sum(aa_counts.values()) # length of the sequence + + # counts of variables + aa_variables_counts['AC'] = aa_counts['A'] + aa_counts['C'] + aa_variables_counts['APGC'] = aa_counts['A'] + aa_counts['P'] + aa_counts['G'] + aa_counts['C'] + aa_variables_counts['AVLIM'] = aa_counts['A'] + aa_counts['V'] + aa_counts['L'] + aa_counts['I'] + aa_counts['M'] + aa_variables_counts['AVLIMFYW'] = aa_variables_counts['AVLIM'] + aa_counts['F'] + aa_counts['Y'] + aa_counts['W'] + aa_variables_counts['DE'] = aa_counts['D'] + aa_counts['E'] + aa_variables_counts['DNQTSHA'] = aa_counts['D'] + aa_counts['N'] + aa_counts['Q'] + aa_counts['T'] + aa_counts['S'] + aa_counts['H'] + aa_counts['A'] + aa_variables_counts['EK'] = aa_counts['E'] + aa_counts['K'] + aa_variables_counts['ERK'] = aa_counts['E'] + aa_counts['K'] + aa_counts['K'] + aa_variables_counts['FYMINK'] = aa_counts['F'] + aa_counts['Y'] + aa_counts['M'] + aa_counts['I'] + aa_counts['N'] + aa_counts['K'] + aa_variables_counts['FYW'] = aa_counts['F'] + aa_counts['Y'] + aa_counts['W'] + aa_variables_counts['GARP'] = aa_counts['G'] + aa_counts['A'] + aa_counts['R'] + aa_counts['P'] + aa_variables_counts['IVYWREL'] = aa_counts['I'] + aa_counts['V'] + aa_counts['Y'] + aa_counts['W'] + aa_counts['R'] + aa_counts['E'] + aa_counts['L'] + aa_variables_counts['QH'] = aa_counts['Q'] + aa_counts['H'] + aa_variables_counts['RHK'] = aa_counts['R'] + aa_counts['H'] + aa_counts['K'] + aa_variables_counts['RHKDE'] = aa_counts['R'] + aa_counts['H'] + aa_counts['K'] + aa_counts['D'] + aa_counts['E'] + aa_variables_counts['STNQ'] = aa_counts['S'] + aa_counts['T'] + aa_counts['N'] + aa_counts['Q'] + aa_variables_counts['VLIM'] = aa_counts['V'] + aa_counts['L'] + aa_counts['I'] + aa_counts['M'] + aa_variables_counts['PAYRE'] = aa_counts['P'] + aa_counts['A'] + aa_counts['Y'] + aa_counts['R'] + aa_counts['E'] + aa_variables_counts['MVGDS'] = aa_counts['M'] + aa_counts['V'] + aa_counts['G'] + aa_counts['D'] + aa_counts['S'] + + # compute proportions + for key in aa_variables_counts.keys(): + aa_variables_props[key] = float(aa_variables_counts[key]) / float(len_seq) + + if aa_variables_counts['DNQTSHA'] != 0: + ratio_ERK_DNQTSHA = float(aa_variables_counts['ERK'])/float(aa_variables_counts['DNQTSHA']) + else : + ratio_ERK_DNQTSHA = -1 + + if aa_variables_counts['QH'] != 0: + ratio_EK_QH = float(aa_variables_counts['EK'])/float(aa_variables_counts['QH']) + else : + ratio_EK_QH = -1 + + if aa_variables_counts['FYMINK'] != 0: + ratio_GARP_FYMINK = float(aa_variables_counts['EK'])/float(aa_variables_counts['FYMINK']) + else : + ratio_GARP_FYMINK = -1 + + if aa_variables_counts['VLIM'] != 0: + ratio_AC_VLIM = float(aa_variables_counts['AC'])/float(aa_variables_counts['VLIM']) + ratio_APGC_VLIM = float(aa_variables_counts['APGC'])/float(aa_variables_counts['VLIM']) + else : + ratio_AC_VLIM = -1 + ratio_APGC_VLIM = -1 + + if aa_variables_counts['MVGDS'] != 0: + ratio_PAYRE_MVGDS = float(aa_variables_counts['PAYRE'])/float(aa_variables_counts['MVGDS']) + else : + ratio_PAYRE_MVGDS = -1 + + if aa_variables_counts['MVGDS'] != 0: + ratio_AC_MVGDS = float(aa_variables_counts['AC'])/float(aa_variables_counts['MVGDS']) + else : + ratio_AC_MVGDS = -1 + + aa_variables_counts['ratio_ERK_DNQTSHA'] = ratio_ERK_DNQTSHA + aa_variables_counts['ratio_EK_QH'] = ratio_EK_QH + aa_variables_counts['ratio_GARP_FYMINK'] = ratio_GARP_FYMINK + aa_variables_counts['ratio_AC_VLIM'] = ratio_AC_VLIM + aa_variables_counts['ratio_APGC_VLIM'] = ratio_APGC_VLIM + aa_variables_counts['ratio_PAYRE_MVGDS'] = ratio_PAYRE_MVGDS + aa_variables_counts['ratio_AC_MVGDS'] = ratio_AC_MVGDS + + return aa_variables_counts, aa_variables_props + +def sequence_properties_from_aa_properties(aa_counts, aa_properties): + """ Computes a sequence properties (based on an external data file) + + Args: + - aa_counts (dict) : counts of amino-acids in the sequence + - aa_properties (dict) : key/amino-acid - value/list of properties extract from the external data file + + Returns: + - seq_props (dict) : values of the sequence properties + """ + + LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation'] + seq_props = {} + + for i in range(1,5): + seq_props[LS[i-1]] = 0 + for key in aa_counts.keys(): + seq_props[LS[i-1]] += aa_counts[key] * float(aa_properties[key][i]) + + return seq_props + +""" Main """ + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("species_list", help="List of species separated by commas") + parser.add_argument("aa_properties", help="File with all amino-acids properties") + args = parser.parse_args() + + LAA = ['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G'] + LV = ['IVYWREL','EK','ERK','DNQTSHA','QH','ratio_ERK_DNQTSHA','ratio_EK_QH','FYMINK','GARP', + 'ratio_GARP_FYMINK','AVLIM','FYW','AVLIMFYW','STNQ','RHK','DE','RHKDE','APGC','AC', + 'VLIM','ratio_AC_VLIM','ratio_APGC_VLIM'] + LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation'] + + list_inputs = [] + + path_inputs = '01_input_files' + list_inputs = os.listdir(path_inputs) + + lsp = args.species_list.split(',') + lsp = sorted(lsp) + flsp = '' + for el in lsp: + flsp += el+',' + + path_outputs_1 = '02_tables_per_aa' + path_outputs_2 = '02_tables_per_aa_variable' + os.mkdir(path_outputs_1) + os.mkdir(path_outputs_2) + + # Init empty dicts for results + dict_for_files_aa_counts = {} # counts + dict_for_files_aa_props = {} # proportions + dict_for_files_variables_counts = {} + dict_for_files_variables_props = {} + dict_for_files_seq_properties = {} + + aa_properties_file = aa_properties(args.aa_properties) # read the aa_properties file + + # All counts and props + for file in list_inputs: + # iterate over input files + sequences = dico(file, path_inputs) + + # TEMPORARY CORRECTION FOR SEQUENCES CONTAINING ONLY INDELS + # It appears than CDS_Search can bug sometimes and return an alignement where a species' sequence is made of indels only + # This causes a crash here (in the ratios function). The correction skip the whole file. + # When CDS_Search is corrected, lines with 'skip' can be removed + skip = False + for key in sequences.keys(): + if all(x == '-' for x in sequences[key]): + skip = True + + if not skip: + + aa_counts_per_seq = {} + aa_props_per_seq = {} + aa_variables_counts_per_seq = {} + aa_variables_props_per_seq = {} + seq_properties = {} + + for key in sequences.keys(): + # iterate over sequences in the file + aa_counts_per_seq[key] = all_aa_counts(sequences[key]) + aa_props_per_seq[key] = all_aa_props(aa_counts_per_seq[key]) + aa_variables_counts_per_seq[key], aa_variables_props_per_seq[key] = aa_variables_counts_and_props(aa_counts_per_seq[key]) + seq_properties[key] = sequence_properties_from_aa_properties(aa_counts_per_seq[key], aa_properties_file) + + # Add NaN for missing species + for key in set(lsp).difference(set(sequences.keys())): + aa_counts_per_seq[key] = fill_with_NaN(LAA) + aa_props_per_seq[key] = fill_with_NaN(LAA) + aa_variables_counts_per_seq[key] = fill_with_NaN(LV) + seq_properties[key] = fill_with_NaN(LS) + + # Add computations to final dicts + dict_for_files_aa_counts[file] = aa_counts_per_seq + dict_for_files_aa_props[file] = aa_props_per_seq + dict_for_files_variables_counts[file] = aa_variables_counts_per_seq + dict_for_files_variables_props[file] = aa_variables_props_per_seq + dict_for_files_seq_properties[file] = seq_properties + + # Try with pandas ? + write_output(LAA, flsp, path_outputs_1, dict_for_files_aa_counts) # one file per AA + write_output(LV, flsp, path_outputs_2, dict_for_files_variables_counts) # one file per aa_variable + write_output(LS, flsp, path_outputs_2, dict_for_files_seq_properties) #one file per seq properties + + # { file_name1 : { seq1: {'A' : 0, 'C':0, 'E':0, ...}, + # seq2: {'A' : 0, 'C':0, 'E':0, ...}, ... + # }, + # { file_name2 : { seq1: {'A' : 0, 'C':0, 'E':0, ...}, + # seq2: {'A' : 0, 'C':0, 'E':0, ...}, + # }, + # ... } + + # { file_name1 : {seq1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # seq2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, ... + # }, + # file_name2 : {seq1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # seq2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # }, + # ... } + + # { file_name1 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # file_name2 : {'IVYWREL' : 0, 'EK': 0, 'ERK': 0, ...}, + # ... + # } + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S02b_extreme_2states.py Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,159 @@ +#!/usr/bin/env python +#coding: utf-8 +#Author : Eric Fontanillas (2010) - Victor Mataigne (2018) + +import pandas as pd +import argparse, os + +def loop_on_elems(list_of_elems, path_in, path_out, sps_group_1, sps_group_2, colnames): + + # sub-routine + + def tableu(fileu, sps_group_1, sps_group_2): + """ a + + Args : + fileu : input file with counts of AAs / AAs types per orthogorup + sps_group_1 : species for condition 1 (ex : hot water species) + sps_group_2 : species for condition 2 (ex : cold water species) + + Returns : + greater_dict : + lower_dict : + + """ + df = pd.read_csv(fileu, sep=',', index_col=0, header=0) + # species = list(df) #columns names = species names + + # initialize counts + greater_dict = {} + lower_dict = {} + + for specie in sps_group_1+sps_group_2: + greater_dict[specie] = 0 + lower_dict[specie] = 0 + + #nb_trials = 0 + for (index, row) in df.iterrows(): + # min and max counts for each condition + if not df.loc[index, sps_group_1+sps_group_2].isnull().values.any() : + #nb_trials += 1 + + max_cat1 = max(df.loc[index, sps_group_1]) # species in category 1 (ex : hots) + min_cat1 = min(df.loc[index, sps_group_1]) + max_cat2 = max(df.loc[index, sps_group_2]) # species in category 2 (ex : colds) + min_cat2 = min(df.loc[index, sps_group_2]) + + for specie in sps_group_1: + if df.loc[index, specie] > max_cat2 : + greater_dict[specie] += 1 + elif df.loc[index, specie] < min_cat2 : + lower_dict[specie] += 1 + + for specie in sps_group_2: + if df.loc[index, specie] > max_cat1 : + greater_dict[specie] += 1 + elif df.loc[index, specie] < min_cat1 : + lower_dict[specie] += 1 + + return greater_dict, lower_dict#, nb_trials + + # Function ------------------------------------------------------ + + for variable in list_of_elems: + print 'Processing : {} ...'.format(variable) + file_in = "{}/{}.csv".format(path_in, variable) + file_out = open('{}/{}.csv'.format(path_out,variable), 'w') + + # Compute succeses and fails on each variable + greater_dict, lower_dict = tableu(file_in, sps_group_1, sps_group_2) + + # totals and diffs + diff_dict = {} + total_dict = {} + for key in greater_dict.keys(): + diff_dict[key] = greater_dict[key] - lower_dict[key] + total_dict[key] = greater_dict[key] + lower_dict[key] + #total_dict[key] = number_trials + + # results frame + df = pd.DataFrame([greater_dict, lower_dict, diff_dict, total_dict]) + df = df.rename({0:'Greater',1:'Lower',2:'Difference',3:'Trial_Number'}) #, axis='index' if pandas 0.15 + df = df.rename(index=str, columns=colnames) + + df.to_csv("{}/{}.csv".format(path_out, variable), sep=",", encoding="utf-8") + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument("sps_group_1", help="List of species separated by commas") + parser.add_argument("sps_group_2", help="List of species separated by commas") + parser.add_argument("format", choices=['nucleic', 'proteic'], help="input files format") + args = parser.parse_args() + + # used only if format = nucleic + LN =['A','C','T','G'] + Lratios = ['GC_percent', 'purine_percent', 'DIFF_GC', 'DIFF_AT', 'PLI_GC', 'PLI_AT', 'PLI_GC_1000', 'PLI_AT_1000'] + + # used only if format = proteic + LAA =['K','R','A','F','I','L','M','V','W','N','Q','S','T','H','Y','C','D','E','P','G'] + LV = ['IVYWREL','EK','ERK','DNQTSHA','QH','ratio_ERK_DNQTSHA','ratio_EK_QH','FYMINK','GARP', + 'ratio_GARP_FYMINK','AVLIM','FYW','AVLIMFYW','STNQ','RHK','DE','RHKDE','APGC','AC', + 'VLIM','ratio_AC_VLIM','ratio_APGC_VLIM'] + LS = ['total_residue_weight', 'total_residue_volume', 'total_partial_specific_volume', 'total_hydratation'] + + # inputs and outputs paths + if args.format == 'nucleic': + input_path_elem = '02_tables_per_nucleotide' + input_path_var = '02_tables_per_nuc_variable' + out_path_elem = '03_tables_counts_signTest_nucleotides' + out_path_var = '03_tables_counts_signTest_nuc_variables' + elif args.format == 'proteic': + input_path_elem = '02_tables_per_aa' + input_path_var = '02_tables_per_aa_variable' + out_path_elem = '03_tables_counts_signTest_aa' + out_path_var = '03_tables_counts_signTest_aa_variables' + + os.mkdir(out_path_elem) + os.mkdir(out_path_var) + + sps_group_1 = args.sps_group_1.split(',') + sps_group_2 = args.sps_group_2.split(',') + + # Prepare colnames for final frames + colnames = {} + # for specie in sps_group_1: + # colnames[specie] = '{}_vs_condition_1'.format(specie) + # for specie in sps_group_2: + # colnames[specie] = '{}_vs_condition_2'.format(specie) + + for specie in sps_group_1: + colnames[specie] = '{}_vs_{}'.format(specie, args.sps_group_2.replace(',','')) + for specie in sps_group_2: + colnames[specie] = '{}_vs_{}'.format(specie, args.sps_group_1.replace(',','')) + + # Building tables + if args.format == 'nucleic': + loop_on_elems(LN, input_path_elem, out_path_elem, sps_group_1, sps_group_2, colnames) + loop_on_elems(Lratios, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames) + elif args.format == 'proteic': + loop_on_elems(LAA, input_path_elem, out_path_elem, sps_group_1, sps_group_2, colnames) + loop_on_elems(LV, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames) + loop_on_elems(LS, input_path_var, out_path_var, sps_group_1, sps_group_2, colnames) + + # Final R script launching sign test + print 'Processing : binomial sign tests ...' + + if args.format == 'nucleic': + final_output_elem = '04_outputs_nucleotides' + final_output_var = '04_outputs_nuc_variables' + elif args.format == 'proteic': + final_output_elem = '04_outputs_aa' + final_output_var = '04_outputs_aa_variables' + + os.mkdir(final_output_elem) + os.mkdir(final_output_var) + os.system('Rscript S03b_sign_test_binomial.R --indir %s --outdir %s' %(out_path_elem, final_output_elem)) + os.system('Rscript S03b_sign_test_binomial.R --indir %s --outdir %s' %(out_path_var, final_output_var)) + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S03b_sign_test_binomial.R Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,56 @@ +#!/usr/bin/env Rscript +#coding: utf-8 +#Author : Eric Fontanillas (2010) - Victor Mataigne (2018) + +# binom test - null hypothesis : +# The test computes the number of times where the value of the variable A is higher to the value of the variable B. +# Under the null hypothesis, there is no difference between variables : A > B in 50% of the trials + +options(warn = -1) + +library(optparse) + +option_list = list( + make_option(c('-i', '--indir'), type='character', default=NULL, help='input directory name', metavar='character'), + make_option(c('-o', '--outdir'), type='character', default=NULL, help='output directory name', metavar='character') +); + +opt_parser = OptionParser(option_list=option_list); +opt = parse_args(opt_parser); +path_IN <- opt$indir +path_OUT <- opt$outdir +files_OUT <- paste(path_OUT,"/*",sep='') +unlink(files_OUT) ### clean the path_OUT folder from previous files +list_files <- list.files(path_IN) + +# iterate over file +for(file in list_files){ + name_OUT = paste(path_OUT,"/", file, sep='') + name_IN = paste(path_IN,"/", file, sep='') + + b <- read.table(name_IN, sep=",", header=T, row.names=1) + + supplemental_cells <- matrix(0, nrow=4, ncol=ncol(b)) + colnames(supplemental_cells) <- colnames(b) + row.names(supplemental_cells) <- c('p-value', 'probability_of_success', 'confidence_interval_low', 'confidence_interval_high') + + # iterate over species groups + for (i in 1:ncol(b)) { + if (b[4,i] != 0) { + binom_test <- binom.test(b[1,i], b[4,i]) + supplemental_cells[1,i] <- binom_test$p.value + supplemental_cells[2,i] <- binom_test$estimate + supplemental_cells[3,i] <- binom_test$conf.int[1] + supplemental_cells[4,i] <- binom_test$conf.int[2] + } else { + supplemental_cells[1,i] <- NA + supplemental_cells[2,i] <- NA + supplemental_cells[3,i] <- NA + supplemental_cells[4,i] <- NA + } + } + + final <- rbind(b, supplemental_cells) + write.csv(final, file=name_OUT) +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/amino_acid_properties.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,21 @@ +Groups,Amino Acid (Codes),Frequency,Genetic Codons,Substitution Probabilities (each > sign = factor of 10> than random chance),Residue Weight(Mr) (UNIT:Daltons),Residue Volume(Vr) (UNIT:cubic Angstroms),Partial Specific Volume(vr) (UNIT:cc/g),Hydration(hr)(UNIT:moles/mole),R-Group pKa,Extinction Coefficient @ maximum wavelength +Acidic R-groups,Aspartate (Asp/D),5.30%,GAU/GAC,E>N Q>G H,114.08,91,0.6,6,4.5, +Acidic R-groups,Glutamate (Glu/E),6.20%,GAA/GAG,D>Q>HN,128.11,109,0.66,7.5,4.6, +Basic R-groups,Lysine (Lys/K),5.70%,AAA/AAG,R >> N Q,129.19,135,0.82,4.5,10.4, +Basic R-groups,Arginine (Arg /R),5.70%,CGU/CGC/CGA/CGG/AGA/AGG,K>WH>Q,157.2,148,0.7,3,~12, +Basic R-groups,Histidine (His /H),2.30%,CAU/CAC,Q>NR>DE,138.16,118,0.67,4,6.2,5860 @ 211.3 +Polar Uncharged (No H-bonding),Glycine (Gly /G),7.20%,GGU/GGC/GGA/GGG,ADS,57.07,48,0.64,1,, +Polar Uncharged (H-bonding),Serine (Ser /S),6.90%,UCU/UCC/UCA/UCG/AGU/AGC,AGNPT,87.09,73,0.74,2,, +Polar Uncharged (H-bonding),Threonine (Thr /T),5.80%,ACU/ACC/ACA/ACG,AS,101.12,93,0.7,2,, +Polar Uncharged (H-bonding),Cysteine (Cys /C),1.70%,UGU/UGC,none,103.15,86,0.61,1,9.1 to 9.5, +Polar Uncharged (H-bonding),Tyrosine (Tyr /Y),3.20%,UAU/UAC,F >>>>>>,163.12,141,0.61,3,9.6,1420 @ 274.6 +Polar Uncharged (H-bonding),Asparagine (Asn /N),4.40%,AAU/AAC,D H >K,114.1,96,0.62,2,, +Polar Uncharged (H-bonding),Glutamine (Gln /Q),4.00%,CAA/CAG,H >D,128.14,114,0.67,2,, +Non-Polar,Alanine (Ala /A),8.30%,GCU/GCC/GCA/GCG,GSTP,71.09,67,0.74,1,, +Non-Polar,Valine (Val /V),6.60%,GUU/GUC/GUA/GUG,I >>L M >>,99.15,105,0.86,1,, +Non-Polar,Leucine (Leu /L),9.00%,UUA/UUG/CUU/CUG/CUA/CUG,M >>F I V >>,113.18,124,0.9,1,, +Non-Polar,Isoleucine (Ile /I),5.20%,AUU/AUC/AUA,V >> M L > F,113.18,124,0.9,1,, +Non-Polar,Proline (Pro/P),5.10%,CCU/CCC/CCA/CCG,AS,97.13,90,0.76,3,, +Non-Polar,Phenylalanine (Phe /F),3.90%,UUU/UUC,Y>>>>>L> I,147.19,135,0.77,0,,197 @ 257.4 +Non-Polar,Tryptophane (Trp /W),1.30%,UGG,R>,186.23,163,0.74,2,,5600 @ 279.8 +Non-Polar,Methionine (Met /M),2.40%,AUG,L>> I V>>,131.21,124,0.75,1,,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/functions.py Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,65 @@ +#!/usr/bin/env python +#coding: utf-8 + +import itertools, os + +def dico(fasta_file, path_in): + """ + Stores a fasta file in a dictionary : key/value -> header/sequence + + Args: + - fasta_file (String) : the name of fasta file + - path_in (String) : path to the fasta file + + Return: + - bash1 (dict) : the dictionary header/sequence + """ + bash1 = {} + + with open(path_in+'/'+fasta_file, 'r') as F1: + for h,s in itertools.izip_longest(*[F1]*2): + fasta_name = h[1:3] + sequence = s[:-1] + if fasta_name not in bash1.keys(): + bash1[fasta_name] = sequence + else: + print fasta_name + + return bash1 # same length for all (alignment) + +def write_output(names, sps_list, out_dir, results_dict): + """ Write results in csv files. There is one file per counted element (one file per amino-acid, one file per indice ...) + + Args: + - names (list) : list with the names of elems + - sps_list (list) : species names, sorted alphabetically + - out_dir (String) : output directory + - results_dict (dict) : vcounts values of each element for each input file (keys names : elems from 'names argument') + + """ + for name in names: + out = open(name+".csv", 'w') + out.write('Group,' + sps_list[0:-1]+'\n') + for group in results_dict.keys(): + count_of_elems = '' + for specs in sorted(results_dict[group].keys()): + count_of_elems += str(results_dict[group][specs][name]) + ',' + out.write(group + ',' + count_of_elems[0:-1] + '\n') + out.close() + os.system('mv %s.csv %s/' %(name, out_dir)) + +def fill_with_NaN(what): + """ Used to create a dict only with NaN values ; used when a species is not present in an orthogroup + + Args: + - what (list of Strings) : the names of the elements studied (nucleotide, amino-acids, indices of thermostability ...) + + Return: + - NaN_values (dict) : dictionary with keys=elems of what, values=NaN + """ + + NaN_values = {} + for elem in what: + NaN_values[elem] = 'NaN' + + return NaN_values
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/A.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,2,2,2,2,2 +locus_6sp_60.fasta,2,2,2,2,2,2 +locus_6sp_40.fasta,8,7,7,6,8,7 +locus_6sp_58.fasta,1,1,0,0,1,0 +locus_6sp_38.fasta,4,4,5,4,2,3 +locus_4sp_4.fasta,3,NaN,2,2,2,NaN +locus_4sp_6.fasta,0,1,0,0,NaN,NaN +locus_6sp_27.fasta,1,1,1,0,1,0 +locus_6sp_41.fasta,5,5,5,5,6,5 +locus_6sp_39.fasta,3,3,4,3,3,4 +locus_6sp_10.fasta,5,5,5,5,4,5 +locus_6sp_25.fasta,19,18,20,17,19,18 +locus_6sp_32.fasta,8,8,10,8,8,10 +locus_6sp_53.fasta,7,6,6,6,6,7 +locus_3sp_2.fasta,NaN,3,NaN,3,4,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,4,3,3,3,4,3 +locus_6sp_11.fasta,14,14,12,13,13,13 +locus_6sp_35.fasta,3,3,4,3,3,3 +locus_6sp_46.fasta,7,7,7,6,5,8 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,9,9,8,7,8,9 +locus_6sp_50.fasta,35,34,35,37,36,36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/C.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,1,1,1,1,1,1 +locus_6sp_40.fasta,0,0,1,0,0,1 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,0,0 +locus_4sp_4.fasta,3,NaN,5,4,5,NaN +locus_4sp_6.fasta,13,13,13,13,NaN,NaN +locus_6sp_27.fasta,1,2,2,2,1,2 +locus_6sp_41.fasta,2,2,2,2,2,2 +locus_6sp_39.fasta,0,0,0,0,0,0 +locus_6sp_10.fasta,3,3,3,3,3,3 +locus_6sp_25.fasta,1,1,1,1,1,1 +locus_6sp_32.fasta,1,1,1,1,1,1 +locus_6sp_53.fasta,0,0,0,0,0,1 +locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN +locus_6sp_47.fasta,0,0,0,0,0,0 +locus_6sp_16.fasta,1,1,1,1,1,1 +locus_6sp_11.fasta,2,2,2,2,2,2 +locus_6sp_35.fasta,5,5,2,4,3,4 +locus_6sp_46.fasta,0,0,0,0,0,0 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,1,1,1,1,1,1 +locus_6sp_50.fasta,3,3,3,3,3,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/D.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,2,2,2,3,2,2 +locus_6sp_40.fasta,6,5,4,4,6,3 +locus_6sp_58.fasta,3,3,3,3,3,3 +locus_6sp_38.fasta,5,5,4,6,6,5 +locus_4sp_4.fasta,1,NaN,2,1,2,NaN +locus_4sp_6.fasta,7,7,6,7,NaN,NaN +locus_6sp_27.fasta,1,1,1,1,0,1 +locus_6sp_41.fasta,2,2,2,2,2,2 +locus_6sp_39.fasta,2,2,2,2,2,2 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,23,23,23,23,22,24 +locus_6sp_32.fasta,7,7,6,6,7,5 +locus_6sp_53.fasta,4,4,4,3,3,5 +locus_3sp_2.fasta,NaN,4,NaN,3,3,NaN +locus_6sp_47.fasta,4,4,4,4,4,4 +locus_6sp_16.fasta,3,3,3,2,5,3 +locus_6sp_11.fasta,9,9,9,8,8,8 +locus_6sp_35.fasta,1,1,1,1,1,1 +locus_6sp_46.fasta,4,4,3,4,4,3 +locus_3sp_7.fasta,4,5,4,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,4,4,5,4,5,4 +locus_6sp_50.fasta,7,8,7,7,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/E.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,2,2,2,1,2,2 +locus_6sp_40.fasta,7,8,9,8,7,9 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,7,7,8,6,6,7 +locus_4sp_4.fasta,1,NaN,1,1,1,NaN +locus_4sp_6.fasta,7,7,8,7,NaN,NaN +locus_6sp_27.fasta,0,0,2,0,1,0 +locus_6sp_41.fasta,1,1,1,1,1,1 +locus_6sp_39.fasta,5,4,5,4,4,5 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,18,18,19,17,17,18 +locus_6sp_32.fasta,12,12,13,15,12,14 +locus_6sp_53.fasta,13,13,13,13,12,12 +locus_3sp_2.fasta,NaN,1,NaN,2,1,NaN +locus_6sp_47.fasta,2,2,2,2,2,2 +locus_6sp_16.fasta,6,6,5,6,6,5 +locus_6sp_11.fasta,13,13,13,14,13,13 +locus_6sp_35.fasta,1,1,1,1,1,1 +locus_6sp_46.fasta,22,22,24,22,22,23 +locus_3sp_7.fasta,3,2,3,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,3,2 +locus_6sp_57.fasta,8,8,7,8,7,8 +locus_6sp_50.fasta,4,3,3,4,3,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/F.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,3,3,3,3,3,3 +locus_6sp_40.fasta,2,2,2,2,2,2 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,1,1,1,1,2,1 +locus_4sp_4.fasta,5,NaN,6,7,7,NaN +locus_4sp_6.fasta,2,2,2,1,NaN,NaN +locus_6sp_27.fasta,3,3,1,1,2,2 +locus_6sp_41.fasta,4,4,4,5,5,5 +locus_6sp_39.fasta,5,6,6,6,4,6 +locus_6sp_10.fasta,6,6,6,6,7,6 +locus_6sp_25.fasta,15,15,15,16,15,16 +locus_6sp_32.fasta,8,8,9,9,9,9 +locus_6sp_53.fasta,11,11,11,10,11,9 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,0,0,0,0,0,0 +locus_6sp_16.fasta,2,2,1,2,2,1 +locus_6sp_11.fasta,6,6,6,5,7,6 +locus_6sp_35.fasta,8,8,9,7,8,11 +locus_6sp_46.fasta,7,6,6,6,6,6 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,1,1,2,2,1,2 +locus_6sp_50.fasta,9,9,10,9,9,9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/G.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,3,3,3,3 +locus_6sp_60.fasta,3,3,3,4,3,3 +locus_6sp_40.fasta,9,9,10,10,9,10 +locus_6sp_58.fasta,4,4,4,4,4,4 +locus_6sp_38.fasta,3,3,3,3,3,3 +locus_4sp_4.fasta,1,NaN,1,1,1,NaN +locus_4sp_6.fasta,6,6,6,6,NaN,NaN +locus_6sp_27.fasta,1,1,0,0,1,1 +locus_6sp_41.fasta,3,3,3,3,3,3 +locus_6sp_39.fasta,2,2,2,2,3,2 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,24,24,25,25,23,25 +locus_6sp_32.fasta,6,6,6,6,7,6 +locus_6sp_53.fasta,9,9,9,9,10,9 +locus_3sp_2.fasta,NaN,4,NaN,4,4,NaN +locus_6sp_47.fasta,7,7,7,7,8,7 +locus_6sp_16.fasta,5,5,5,5,5,5 +locus_6sp_11.fasta,15,15,15,14,15,15 +locus_6sp_35.fasta,5,5,5,6,5,6 +locus_6sp_46.fasta,4,4,4,3,3,3 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,8,8,8,8,8,8 +locus_6sp_50.fasta,39,39,39,39,40,39
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/H.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,2,2,2,3,2,3 +locus_6sp_58.fasta,1,1,1,2,1,1 +locus_6sp_38.fasta,11,11,10,10,8,10 +locus_4sp_4.fasta,6,NaN,4,4,5,NaN +locus_4sp_6.fasta,2,3,2,3,NaN,NaN +locus_6sp_27.fasta,3,3,3,3,2,3 +locus_6sp_41.fasta,1,1,1,1,0,1 +locus_6sp_39.fasta,4,4,4,4,3,4 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,10,10,11,10,10,11 +locus_6sp_32.fasta,1,1,2,2,1,1 +locus_6sp_53.fasta,3,3,5,3,3,1 +locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,1,1,1,1,1,1 +locus_6sp_11.fasta,0,1,1,1,1,0 +locus_6sp_35.fasta,2,2,2,2,2,3 +locus_6sp_46.fasta,0,0,0,0,0,0 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,2,2,2,2,2,2 +locus_6sp_50.fasta,2,2,2,3,3,2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/I.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,1,1,1,1,1,1 +locus_6sp_40.fasta,5,4,5,3,5,4 +locus_6sp_58.fasta,1,1,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,1,0 +locus_4sp_4.fasta,7,NaN,9,9,9,NaN +locus_4sp_6.fasta,6,7,6,6,NaN,NaN +locus_6sp_27.fasta,0,0,1,1,3,2 +locus_6sp_41.fasta,5,5,5,6,5,6 +locus_6sp_39.fasta,4,3,4,3,4,4 +locus_6sp_10.fasta,5,5,5,5,5,5 +locus_6sp_25.fasta,17,16,15,15,15,15 +locus_6sp_32.fasta,5,4,2,3,1,2 +locus_6sp_53.fasta,8,8,6,8,6,8 +locus_3sp_2.fasta,NaN,0,NaN,1,0,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,3,3,3,4,4,3 +locus_6sp_11.fasta,10,11,12,10,10,11 +locus_6sp_35.fasta,4,5,4,7,7,4 +locus_6sp_46.fasta,10,10,11,9,10,10 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,3,3,3,3,4,3 +locus_6sp_50.fasta,23,22,24,20,20,24
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/K.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,1,1,0,1,1,0 +locus_6sp_40.fasta,9,8,10,10,9,10 +locus_6sp_58.fasta,1,1,1,1,1,1 +locus_6sp_38.fasta,15,15,15,15,15,15 +locus_4sp_4.fasta,1,NaN,1,1,0,NaN +locus_4sp_6.fasta,5,5,8,6,NaN,NaN +locus_6sp_27.fasta,1,1,0,1,0,1 +locus_6sp_41.fasta,1,2,1,1,1,1 +locus_6sp_39.fasta,4,3,3,3,4,3 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,18,17,20,20,21,19 +locus_6sp_32.fasta,19,20,19,19,19,19 +locus_6sp_53.fasta,11,11,10,10,11,10 +locus_3sp_2.fasta,NaN,4,NaN,4,4,NaN +locus_6sp_47.fasta,10,10,10,10,10,10 +locus_6sp_16.fasta,2,2,2,2,2,2 +locus_6sp_11.fasta,16,16,15,15,15,15 +locus_6sp_35.fasta,2,2,2,2,2,2 +locus_6sp_46.fasta,23,24,25,22,26,24 +locus_3sp_7.fasta,4,4,4,NaN,NaN,NaN +locus_6sp_30.fasta,4,4,4,4,3,3 +locus_6sp_57.fasta,5,5,5,5,5,5 +locus_6sp_50.fasta,7,5,6,6,6,6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/L.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,4,3,2,3 +locus_6sp_60.fasta,2,2,1,1,2,1 +locus_6sp_40.fasta,8,7,9,10,9,9 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,1,1,0,0,0,0 +locus_4sp_4.fasta,11,NaN,10,8,10,NaN +locus_4sp_6.fasta,4,4,5,4,NaN,NaN +locus_6sp_27.fasta,9,9,8,9,10,8 +locus_6sp_41.fasta,7,7,7,6,8,8 +locus_6sp_39.fasta,3,3,3,3,5,3 +locus_6sp_10.fasta,2,2,3,2,3,3 +locus_6sp_25.fasta,25,24,24,25,24,26 +locus_6sp_32.fasta,13,14,14,13,14,14 +locus_6sp_53.fasta,6,6,7,7,7,9 +locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN +locus_6sp_47.fasta,6,6,6,6,6,6 +locus_6sp_16.fasta,3,3,3,3,3,3 +locus_6sp_11.fasta,11,11,11,11,11,11 +locus_6sp_35.fasta,8,8,8,6,6,7 +locus_6sp_46.fasta,14,13,13,14,14,13 +locus_3sp_7.fasta,8,8,8,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,8,8,8,8,8,8 +locus_6sp_50.fasta,27,27,26,27,26,26
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/M.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,2,3,3,3 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,9,9,9,9,9,9 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,0,0 +locus_4sp_4.fasta,2,NaN,2,2,5,NaN +locus_4sp_6.fasta,2,2,2,2,NaN,NaN +locus_6sp_27.fasta,0,0,0,1,0,0 +locus_6sp_41.fasta,2,2,2,1,2,1 +locus_6sp_39.fasta,0,0,0,1,0,0 +locus_6sp_10.fasta,5,5,4,5,4,4 +locus_6sp_25.fasta,3,3,3,4,6,4 +locus_6sp_32.fasta,7,7,7,7,9,7 +locus_6sp_53.fasta,1,1,1,1,1,2 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,0,1,0,0,0,0 +locus_6sp_16.fasta,0,0,0,0,0,0 +locus_6sp_11.fasta,6,5,6,6,4,6 +locus_6sp_35.fasta,1,1,2,1,1,2 +locus_6sp_46.fasta,4,4,2,4,3,3 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,4,4,4,4,4,4 +locus_6sp_50.fasta,18,18,19,20,20,20
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/N.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,1,1,2,2,1,2 +locus_6sp_40.fasta,1,1,0,1,0,1 +locus_6sp_58.fasta,1,1,1,1,2,1 +locus_6sp_38.fasta,5,5,5,5,5,5 +locus_4sp_4.fasta,1,NaN,1,3,1,NaN +locus_4sp_6.fasta,6,5,4,4,NaN,NaN +locus_6sp_27.fasta,0,0,0,0,0,0 +locus_6sp_41.fasta,3,2,2,2,2,3 +locus_6sp_39.fasta,2,2,2,2,2,2 +locus_6sp_10.fasta,1,1,1,1,1,1 +locus_6sp_25.fasta,17,19,14,13,17,13 +locus_6sp_32.fasta,3,3,3,3,3,3 +locus_6sp_53.fasta,4,4,4,4,3,5 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,0,0,1,1,0,0 +locus_6sp_11.fasta,6,6,7,7,8,7 +locus_6sp_35.fasta,3,3,1,2,3,2 +locus_6sp_46.fasta,3,3,3,3,4,3 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,2,2,3,3,2,3 +locus_6sp_50.fasta,6,6,7,7,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/P.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,4,4,3,4,4,4 +locus_6sp_58.fasta,0,0,0,1,0,0 +locus_6sp_38.fasta,8,7,7,7,7,7 +locus_4sp_4.fasta,3,NaN,3,3,4,NaN +locus_4sp_6.fasta,4,4,4,4,NaN,NaN +locus_6sp_27.fasta,1,1,2,0,0,2 +locus_6sp_41.fasta,1,1,1,1,1,1 +locus_6sp_39.fasta,2,2,2,2,2,2 +locus_6sp_10.fasta,2,2,2,2,2,2 +locus_6sp_25.fasta,16,15,14,15,14,14 +locus_6sp_32.fasta,4,4,4,4,5,4 +locus_6sp_53.fasta,6,6,6,6,6,5 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,0,0,0,0,0,0 +locus_6sp_16.fasta,1,1,1,1,1,1 +locus_6sp_11.fasta,6,6,6,5,6,6 +locus_6sp_35.fasta,4,4,3,4,3,3 +locus_6sp_46.fasta,2,2,2,2,2,2 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,2,2,2,2,2,2 +locus_6sp_50.fasta,13,13,13,13,13,13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/Q.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,2,2,2,1,2,1 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,2,2,2,2,2,1 +locus_4sp_4.fasta,0,NaN,0,0,0,NaN +locus_4sp_6.fasta,4,4,4,4,NaN,NaN +locus_6sp_27.fasta,2,2,1,2,3,2 +locus_6sp_41.fasta,2,2,2,2,3,2 +locus_6sp_39.fasta,3,4,2,3,4,2 +locus_6sp_10.fasta,1,1,1,1,1,1 +locus_6sp_25.fasta,11,11,10,10,11,8 +locus_6sp_32.fasta,4,3,4,2,3,4 +locus_6sp_53.fasta,4,4,3,5,4,5 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,1,1,2,1,1,2 +locus_6sp_11.fasta,9,8,8,7,7,9 +locus_6sp_35.fasta,0,0,0,0,0,0 +locus_6sp_46.fasta,6,5,6,8,8,7 +locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,3,3,3,3,3,3 +locus_6sp_50.fasta,5,5,5,4,5,5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/R.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,2,2,3,3,2,3 +locus_6sp_40.fasta,7,8,5,5,6,5 +locus_6sp_58.fasta,8,8,8,7,8,8 +locus_6sp_38.fasta,16,16,17,17,19,18 +locus_4sp_4.fasta,5,NaN,5,4,6,NaN +locus_4sp_6.fasta,10,9,8,9,NaN,NaN +locus_6sp_27.fasta,1,0,3,2,2,2 +locus_6sp_41.fasta,6,5,8,7,4,4 +locus_6sp_39.fasta,1,2,4,3,2,4 +locus_6sp_10.fasta,1,1,1,1,1,1 +locus_6sp_25.fasta,12,13,13,11,11,12 +locus_6sp_32.fasta,7,7,6,6,6,6 +locus_6sp_53.fasta,7,7,7,7,6,7 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,10,10,10,10,10,10 +locus_6sp_16.fasta,0,0,0,0,0,0 +locus_6sp_11.fasta,6,6,7,8,7,7 +locus_6sp_35.fasta,2,2,4,3,3,2 +locus_6sp_46.fasta,14,15,14,16,12,15 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,2 +locus_6sp_57.fasta,4,4,5,5,4,5 +locus_6sp_50.fasta,11,12,11,11,10,11
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/S.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,5,5,5,4,5,5 +locus_6sp_40.fasta,7,7,6,6,6,6 +locus_6sp_58.fasta,32,33,34,33,33,34 +locus_6sp_38.fasta,21,21,23,23,21,23 +locus_4sp_4.fasta,5,NaN,3,4,2,NaN +locus_4sp_6.fasta,2,1,1,2,NaN,NaN +locus_6sp_27.fasta,2,2,2,3,1,2 +locus_6sp_41.fasta,11,12,10,11,11,11 +locus_6sp_39.fasta,1,1,1,2,1,1 +locus_6sp_10.fasta,3,3,3,3,3,3 +locus_6sp_25.fasta,14,15,13,17,15,15 +locus_6sp_32.fasta,6,6,5,5,6,5 +locus_6sp_53.fasta,6,6,6,6,8,6 +locus_3sp_2.fasta,NaN,0,NaN,0,0,NaN +locus_6sp_47.fasta,4,4,4,4,3,4 +locus_6sp_16.fasta,3,3,3,3,2,3 +locus_6sp_11.fasta,2,2,3,4,4,3 +locus_6sp_35.fasta,3,3,5,4,6,3 +locus_6sp_46.fasta,3,3,3,4,4,4 +locus_3sp_7.fasta,2,2,1,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,9,9,8,9,10,8 +locus_6sp_50.fasta,15,16,15,14,16,15
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/T.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,1,1,1,1,1,1 +locus_6sp_40.fasta,3,3,4,4,5,3 +locus_6sp_58.fasta,2,1,1,2,1,1 +locus_6sp_38.fasta,5,6,3,4,6,3 +locus_4sp_4.fasta,9,NaN,10,11,7,NaN +locus_4sp_6.fasta,4,4,4,4,NaN,NaN +locus_6sp_27.fasta,1,1,1,2,1,1 +locus_6sp_41.fasta,7,7,7,7,7,7 +locus_6sp_39.fasta,4,5,3,5,3,3 +locus_6sp_10.fasta,5,5,5,5,5,5 +locus_6sp_25.fasta,15,14,17,17,14,17 +locus_6sp_32.fasta,7,7,8,10,6,8 +locus_6sp_53.fasta,7,8,8,8,8,6 +locus_3sp_2.fasta,NaN,2,NaN,2,1,NaN +locus_6sp_47.fasta,4,3,4,4,4,4 +locus_6sp_16.fasta,2,2,2,2,2,3 +locus_6sp_11.fasta,5,5,4,4,7,5 +locus_6sp_35.fasta,5,5,3,4,5,4 +locus_6sp_46.fasta,5,5,2,3,4,3 +locus_3sp_7.fasta,0,0,1,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,7,7,7,7,6,6 +locus_6sp_50.fasta,12,12,12,11,9,12
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/V.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,0,0,0,1,0 +locus_6sp_60.fasta,1,1,1,0,1,1 +locus_6sp_40.fasta,4,7,5,7,4,6 +locus_6sp_58.fasta,0,0,1,0,0,1 +locus_6sp_38.fasta,0,0,1,1,2,3 +locus_4sp_4.fasta,6,NaN,4,4,3,NaN +locus_4sp_6.fasta,2,2,2,3,NaN,NaN +locus_6sp_27.fasta,5,5,4,4,3,3 +locus_6sp_41.fasta,5,5,5,5,5,5 +locus_6sp_39.fasta,3,3,3,2,3,3 +locus_6sp_10.fasta,2,2,2,2,3,2 +locus_6sp_25.fasta,26,28,27,27,28,28 +locus_6sp_32.fasta,8,8,8,8,9,8 +locus_6sp_53.fasta,6,6,7,7,8,6 +locus_3sp_2.fasta,NaN,2,NaN,1,3,NaN +locus_6sp_47.fasta,5,5,5,5,5,5 +locus_6sp_16.fasta,4,5,4,3,2,4 +locus_6sp_11.fasta,10,10,9,11,8,9 +locus_6sp_35.fasta,10,9,10,10,8,9 +locus_6sp_46.fasta,4,5,7,6,5,5 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,10,10,10,10,10,10 +locus_6sp_50.fasta,21,23,20,23,23,19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/W.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0,0,0,0,0,0 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,1,1,1,1,1,1 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,0,0,0,0,0,0 +locus_4sp_4.fasta,0,NaN,0,1,0,NaN +locus_4sp_6.fasta,5,5,5,5,NaN,NaN +locus_6sp_27.fasta,1,1,1,1,1,1 +locus_6sp_41.fasta,1,1,1,1,1,1 +locus_6sp_39.fasta,1,1,0,0,1,0 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,2,2,2,2,2,2 +locus_6sp_32.fasta,1,1,1,1,1,1 +locus_6sp_53.fasta,2,2,2,2,2,2 +locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,0,0,0,0,0,0 +locus_6sp_11.fasta,2,2,2,2,2,2 +locus_6sp_35.fasta,3,3,3,2,3,3 +locus_6sp_46.fasta,3,3,3,3,3,3 +locus_3sp_7.fasta,0,0,0,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,0,0,0,0,0,0 +locus_6sp_50.fasta,3,3,3,3,3,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa/Y.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,2,2,2,2,2,2 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,12,12,12,12,11,12 +locus_4sp_4.fasta,2,NaN,3,2,2,NaN +locus_4sp_6.fasta,5,5,6,6,NaN,NaN +locus_6sp_27.fasta,0,0,0,0,1,0 +locus_6sp_41.fasta,0,0,0,0,0,0 +locus_6sp_39.fasta,3,2,2,2,2,2 +locus_6sp_10.fasta,6,6,6,6,5,6 +locus_6sp_25.fasta,12,12,12,13,13,12 +locus_6sp_32.fasta,5,5,4,4,5,5 +locus_6sp_53.fasta,4,4,4,4,4,4 +locus_3sp_2.fasta,NaN,2,NaN,2,2,NaN +locus_6sp_47.fasta,2,2,2,2,2,2 +locus_6sp_16.fasta,1,1,2,2,1,2 +locus_6sp_11.fasta,1,1,1,2,1,1 +locus_6sp_35.fasta,2,2,3,3,2,2 +locus_6sp_46.fasta,2,2,2,2,2,2 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,3,3,2,2,3,2 +locus_6sp_50.fasta,14,14,14,13,13,14
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/AC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,2,2,2,2,2 +locus_6sp_60.fasta,3,3,3,3,3,3 +locus_6sp_40.fasta,8,7,8,6,8,8 +locus_6sp_58.fasta,1,1,0,0,1,0 +locus_6sp_38.fasta,4,4,5,4,2,3 +locus_4sp_4.fasta,6,NaN,7,6,7,NaN +locus_4sp_6.fasta,13,14,13,13,NaN,NaN +locus_6sp_41.fasta,7,7,7,7,8,7 +locus_6sp_27.fasta,2,3,3,2,2,2 +locus_6sp_39.fasta,3,3,4,3,3,4 +locus_6sp_10.fasta,8,8,8,8,7,8 +locus_6sp_25.fasta,20,19,21,18,20,19 +locus_6sp_32.fasta,9,9,11,9,9,11 +locus_6sp_53.fasta,7,6,6,6,6,8 +locus_3sp_2.fasta,NaN,3,NaN,3,4,NaN +locus_6sp_47.fasta,1,1,1,1,1,1 +locus_6sp_16.fasta,5,4,4,4,5,4 +locus_6sp_11.fasta,16,16,14,15,15,15 +locus_6sp_35.fasta,8,8,6,7,6,7 +locus_6sp_46.fasta,7,7,7,6,5,8 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,1,1,1,1,1,1 +locus_6sp_57.fasta,10,10,9,8,9,10 +locus_6sp_50.fasta,38,37,38,40,39,39
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/APGC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,5,6,6,6,6,6 +locus_6sp_60.fasta,6,6,6,7,6,6 +locus_6sp_40.fasta,21,20,21,20,21,22 +locus_6sp_58.fasta,5,5,4,5,5,4 +locus_6sp_38.fasta,15,14,15,14,12,13 +locus_4sp_4.fasta,10,NaN,11,10,12,NaN +locus_4sp_6.fasta,23,24,23,23,NaN,NaN +locus_6sp_41.fasta,11,11,11,11,12,11 +locus_6sp_27.fasta,4,5,5,2,3,5 +locus_6sp_39.fasta,7,7,8,7,8,8 +locus_6sp_10.fasta,14,14,14,14,13,14 +locus_6sp_25.fasta,60,58,60,58,57,58 +locus_6sp_32.fasta,19,19,21,19,21,21 +locus_6sp_53.fasta,22,21,21,21,22,22 +locus_3sp_2.fasta,NaN,8,NaN,8,9,NaN +locus_6sp_47.fasta,8,8,8,8,9,8 +locus_6sp_16.fasta,11,10,10,10,11,10 +locus_6sp_11.fasta,37,37,35,34,36,36 +locus_6sp_35.fasta,17,17,14,17,14,16 +locus_6sp_46.fasta,13,13,13,11,10,13 +locus_3sp_7.fasta,3,3,3,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,20,20,19,18,19,20 +locus_6sp_50.fasta,90,89,90,92,92,91
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/AVLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,10,10,10,10,10,10 +locus_6sp_60.fasta,6,6,5,4,6,5 +locus_6sp_40.fasta,34,34,35,35,35,35 +locus_6sp_58.fasta,2,2,1,0,1,1 +locus_6sp_38.fasta,5,5,6,5,5,6 +locus_4sp_4.fasta,29,NaN,27,25,29,NaN +locus_4sp_6.fasta,14,16,15,15,NaN,NaN +locus_6sp_41.fasta,24,24,24,23,26,25 +locus_6sp_27.fasta,15,15,14,15,17,13 +locus_6sp_39.fasta,13,12,14,12,15,14 +locus_6sp_10.fasta,19,19,19,19,19,19 +locus_6sp_25.fasta,90,89,89,88,92,91 +locus_6sp_32.fasta,41,41,41,39,41,41 +locus_6sp_53.fasta,28,27,27,29,28,32 +locus_3sp_2.fasta,NaN,8,NaN,8,10,NaN +locus_6sp_47.fasta,15,16,15,15,15,15 +locus_6sp_16.fasta,14,14,13,13,13,13 +locus_6sp_11.fasta,51,51,50,51,46,50 +locus_6sp_35.fasta,26,26,28,27,25,25 +locus_6sp_46.fasta,39,39,40,39,37,39 +locus_3sp_7.fasta,12,12,12,NaN,NaN,NaN +locus_6sp_30.fasta,4,4,4,4,4,4 +locus_6sp_57.fasta,34,34,33,32,34,34 +locus_6sp_50.fasta,124,124,124,127,125,125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/AVLIMFYW.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,12,12,12,12,12,12 +locus_6sp_60.fasta,9,9,8,7,9,8 +locus_6sp_40.fasta,39,39,40,40,40,40 +locus_6sp_58.fasta,2,2,1,0,1,1 +locus_6sp_38.fasta,18,18,19,18,18,19 +locus_4sp_4.fasta,36,NaN,36,35,38,NaN +locus_4sp_6.fasta,26,28,28,27,NaN,NaN +locus_6sp_41.fasta,29,29,29,29,32,31 +locus_6sp_27.fasta,19,19,16,17,21,16 +locus_6sp_39.fasta,22,21,22,20,22,22 +locus_6sp_10.fasta,35,35,35,35,35,35 +locus_6sp_25.fasta,119,118,118,119,122,121 +locus_6sp_32.fasta,55,55,55,53,56,56 +locus_6sp_53.fasta,45,44,44,45,45,47 +locus_3sp_2.fasta,NaN,13,NaN,13,15,NaN +locus_6sp_47.fasta,18,19,18,18,18,18 +locus_6sp_16.fasta,17,17,16,17,16,16 +locus_6sp_11.fasta,60,60,59,60,56,59 +locus_6sp_35.fasta,39,39,43,39,38,41 +locus_6sp_46.fasta,51,50,51,50,48,50 +locus_3sp_7.fasta,13,13,13,NaN,NaN,NaN +locus_6sp_30.fasta,7,7,7,7,7,7 +locus_6sp_57.fasta,38,38,37,36,38,38 +locus_6sp_50.fasta,150,150,151,152,150,151
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/DE.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,4,4,4,4,4,4 +locus_6sp_40.fasta,13,13,13,12,13,12 +locus_6sp_58.fasta,3,3,3,3,3,3 +locus_6sp_38.fasta,12,12,12,12,12,12 +locus_4sp_4.fasta,2,NaN,3,2,3,NaN +locus_4sp_6.fasta,14,14,14,14,NaN,NaN +locus_6sp_41.fasta,3,3,3,3,3,3 +locus_6sp_27.fasta,1,1,3,1,1,1 +locus_6sp_39.fasta,7,6,7,6,6,7 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,41,41,42,40,39,42 +locus_6sp_32.fasta,19,19,19,21,19,19 +locus_6sp_53.fasta,17,17,17,16,15,17 +locus_3sp_2.fasta,NaN,5,NaN,5,4,NaN +locus_6sp_47.fasta,6,6,6,6,6,6 +locus_6sp_16.fasta,9,9,8,8,11,8 +locus_6sp_11.fasta,22,22,22,22,21,21 +locus_6sp_35.fasta,2,2,2,2,2,2 +locus_6sp_46.fasta,26,26,27,26,26,26 +locus_3sp_7.fasta,7,7,7,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,4,3 +locus_6sp_57.fasta,12,12,12,12,12,12 +locus_6sp_50.fasta,11,11,10,11,11,10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,4,5,5,5,5,5 +locus_6sp_60.fasta,11,11,12,12,11,12 +locus_6sp_40.fasta,29,27,25,25,29,24 +locus_6sp_58.fasta,40,40,40,41,41,40 +locus_6sp_38.fasta,53,54,52,54,50,50 +locus_4sp_4.fasta,25,NaN,22,25,19,NaN +locus_4sp_6.fasta,25,25,21,24,NaN,NaN +locus_6sp_41.fasta,31,31,29,30,31,31 +locus_6sp_27.fasta,10,10,9,11,8,9 +locus_6sp_39.fasta,19,21,18,21,18,18 +locus_6sp_10.fasta,19,19,19,19,18,19 +locus_6sp_25.fasta,109,110,108,107,108,106 +locus_6sp_32.fasta,36,35,38,36,34,36 +locus_6sp_53.fasta,35,35,36,35,35,35 +locus_3sp_2.fasta,NaN,11,NaN,10,10,NaN +locus_6sp_47.fasta,20,19,20,20,19,20 +locus_6sp_16.fasta,14,13,15,13,15,15 +locus_6sp_11.fasta,45,45,44,44,48,45 +locus_6sp_35.fasta,17,17,16,16,20,16 +locus_6sp_46.fasta,28,27,24,28,29,28 +locus_3sp_7.fasta,17,18,17,NaN,NaN,NaN +locus_6sp_30.fasta,4,4,4,4,4,4 +locus_6sp_57.fasta,36,36,36,35,36,35 +locus_6sp_50.fasta,82,83,83,83,85,84
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/EK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,3,3,2,2,3,2 +locus_6sp_40.fasta,16,16,19,18,16,19 +locus_6sp_58.fasta,1,1,1,1,1,1 +locus_6sp_38.fasta,22,22,23,21,21,22 +locus_4sp_4.fasta,2,NaN,2,2,1,NaN +locus_4sp_6.fasta,12,12,16,13,NaN,NaN +locus_6sp_41.fasta,2,3,2,2,2,2 +locus_6sp_27.fasta,1,1,2,1,1,1 +locus_6sp_39.fasta,9,7,8,7,8,8 +locus_6sp_10.fasta,4,4,4,4,4,4 +locus_6sp_25.fasta,36,35,39,37,38,37 +locus_6sp_32.fasta,31,32,32,34,31,33 +locus_6sp_53.fasta,24,24,23,23,23,22 +locus_3sp_2.fasta,NaN,5,NaN,6,5,NaN +locus_6sp_47.fasta,12,12,12,12,12,12 +locus_6sp_16.fasta,8,8,7,8,8,7 +locus_6sp_11.fasta,29,29,28,29,28,28 +locus_6sp_35.fasta,3,3,3,3,3,3 +locus_6sp_46.fasta,45,46,49,44,48,47 +locus_3sp_7.fasta,7,6,7,NaN,NaN,NaN +locus_6sp_30.fasta,6,6,6,6,6,5 +locus_6sp_57.fasta,13,13,12,13,12,13 +locus_6sp_50.fasta,11,8,9,10,9,9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ERK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,4,4,2,3,4,2 +locus_6sp_40.fasta,25,24,29,28,25,29 +locus_6sp_58.fasta,2,2,2,2,2,2 +locus_6sp_38.fasta,37,37,38,36,36,37 +locus_4sp_4.fasta,3,NaN,3,3,1,NaN +locus_4sp_6.fasta,17,17,24,19,NaN,NaN +locus_6sp_41.fasta,3,5,3,3,3,3 +locus_6sp_27.fasta,2,2,2,2,1,2 +locus_6sp_39.fasta,13,10,11,10,12,11 +locus_6sp_10.fasta,6,6,6,6,6,6 +locus_6sp_25.fasta,54,52,59,57,59,56 +locus_6sp_32.fasta,50,52,51,53,50,52 +locus_6sp_53.fasta,35,35,33,33,34,32 +locus_3sp_2.fasta,NaN,9,NaN,10,9,NaN +locus_6sp_47.fasta,22,22,22,22,22,22 +locus_6sp_16.fasta,10,10,9,10,10,9 +locus_6sp_11.fasta,45,45,43,44,43,43 +locus_6sp_35.fasta,5,5,5,5,5,5 +locus_6sp_46.fasta,68,70,74,66,74,71 +locus_3sp_7.fasta,11,10,11,NaN,NaN,NaN +locus_6sp_30.fasta,10,10,10,10,9,8 +locus_6sp_57.fasta,18,18,17,18,17,18 +locus_6sp_50.fasta,18,13,15,16,15,15
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/FYMINK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,7,7,6,7,7,7 +locus_6sp_60.fasta,6,6,6,7,6,6 +locus_6sp_40.fasta,28,26,28,27,27,28 +locus_6sp_58.fasta,3,3,2,2,3,2 +locus_6sp_38.fasta,33,33,33,33,34,33 +locus_4sp_4.fasta,18,NaN,22,24,24,NaN +locus_4sp_6.fasta,26,26,28,25,NaN,NaN +locus_6sp_41.fasta,15,15,14,15,15,16 +locus_6sp_27.fasta,4,4,2,4,6,5 +locus_6sp_39.fasta,18,16,17,17,16,17 +locus_6sp_10.fasta,25,25,24,25,24,24 +locus_6sp_25.fasta,82,82,79,81,87,79 +locus_6sp_32.fasta,47,47,44,45,46,45 +locus_6sp_53.fasta,39,39,36,37,36,38 +locus_3sp_2.fasta,NaN,9,NaN,10,9,NaN +locus_6sp_47.fasta,16,17,16,16,16,16 +locus_6sp_16.fasta,8,8,9,11,9,8 +locus_6sp_11.fasta,45,45,47,45,45,46 +locus_6sp_35.fasta,20,21,21,22,23,23 +locus_6sp_46.fasta,49,49,49,46,51,48 +locus_3sp_7.fasta,8,8,8,NaN,NaN,NaN +locus_6sp_30.fasta,9,9,9,9,8,8 +locus_6sp_57.fasta,18,18,19,19,19,19 +locus_6sp_50.fasta,77,74,80,75,76,80
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/FYW.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,3,3,3,3,3,3 +locus_6sp_40.fasta,5,5,5,5,5,5 +locus_6sp_58.fasta,0,0,0,0,0,0 +locus_6sp_38.fasta,13,13,13,13,13,13 +locus_4sp_4.fasta,7,NaN,9,10,9,NaN +locus_4sp_6.fasta,12,12,13,12,NaN,NaN +locus_6sp_41.fasta,5,5,5,6,6,6 +locus_6sp_27.fasta,4,4,2,2,4,3 +locus_6sp_39.fasta,9,9,8,8,7,8 +locus_6sp_10.fasta,16,16,16,16,16,16 +locus_6sp_25.fasta,29,29,29,31,30,30 +locus_6sp_32.fasta,14,14,14,14,15,15 +locus_6sp_53.fasta,17,17,17,16,17,15 +locus_3sp_2.fasta,NaN,5,NaN,5,5,NaN +locus_6sp_47.fasta,3,3,3,3,3,3 +locus_6sp_16.fasta,3,3,3,4,3,3 +locus_6sp_11.fasta,9,9,9,9,10,9 +locus_6sp_35.fasta,13,13,15,12,13,16 +locus_6sp_46.fasta,12,11,11,11,11,11 +locus_3sp_7.fasta,1,1,1,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,3,3 +locus_6sp_57.fasta,4,4,4,4,4,4 +locus_6sp_50.fasta,26,26,27,25,25,26
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/GARP.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,5,6,6,6,6,6 +locus_6sp_60.fasta,7,7,8,9,7,8 +locus_6sp_40.fasta,28,28,25,25,27,26 +locus_6sp_58.fasta,13,13,12,12,13,12 +locus_6sp_38.fasta,31,30,32,31,31,31 +locus_4sp_4.fasta,12,NaN,11,10,13,NaN +locus_4sp_6.fasta,20,20,18,19,NaN,NaN +locus_6sp_41.fasta,15,14,17,16,14,13 +locus_6sp_27.fasta,4,3,6,2,4,5 +locus_6sp_39.fasta,8,9,12,10,10,12 +locus_6sp_10.fasta,12,12,12,12,11,12 +locus_6sp_25.fasta,71,70,72,68,67,69 +locus_6sp_32.fasta,25,25,26,24,26,26 +locus_6sp_53.fasta,29,28,28,28,28,28 +locus_3sp_2.fasta,NaN,9,NaN,9,10,NaN +locus_6sp_47.fasta,18,18,18,18,19,18 +locus_6sp_16.fasta,10,9,9,9,10,9 +locus_6sp_11.fasta,41,41,40,40,41,41 +locus_6sp_35.fasta,14,14,16,16,14,14 +locus_6sp_46.fasta,27,28,27,27,22,28 +locus_3sp_7.fasta,4,4,4,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,3,4 +locus_6sp_57.fasta,23,23,23,22,22,24 +locus_6sp_50.fasta,98,98,98,100,99,99
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/IVYWREL.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,10,9,10,9,9,9 +locus_6sp_60.fasta,8,8,8,6,8,8 +locus_6sp_40.fasta,34,37,36,36,34,36 +locus_6sp_58.fasta,9,9,9,7,8,9 +locus_6sp_38.fasta,36,36,38,36,39,40 +locus_4sp_4.fasta,32,NaN,32,29,31,NaN +locus_4sp_6.fasta,39,39,40,40,NaN,NaN +locus_6sp_41.fasta,25,24,27,26,24,25 +locus_6sp_27.fasta,16,15,19,17,21,16 +locus_6sp_39.fasta,20,18,21,17,21,21 +locus_6sp_10.fasta,22,22,23,22,23,23 +locus_6sp_25.fasta,112,113,112,110,110,113 +locus_6sp_32.fasta,51,51,48,50,48,50 +locus_6sp_53.fasta,46,46,46,48,45,48 +locus_3sp_2.fasta,NaN,10,NaN,11,11,NaN +locus_6sp_47.fasta,29,29,29,29,29,29 +locus_6sp_16.fasta,17,18,17,18,16,17 +locus_6sp_11.fasta,53,54,55,58,52,54 +locus_6sp_35.fasta,30,30,33,32,30,28 +locus_6sp_46.fasta,69,70,74,72,68,71 +locus_3sp_7.fasta,14,13,14,NaN,NaN,NaN +locus_6sp_30.fasta,6,6,6,6,7,7 +locus_6sp_57.fasta,36,36,35,36,36,36 +locus_6sp_50.fasta,103,104,101,101,98,100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/QH.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,0,0,0,0,0,0 +locus_6sp_40.fasta,4,4,4,4,4,4 +locus_6sp_58.fasta,1,1,1,2,1,1 +locus_6sp_38.fasta,13,13,12,12,10,11 +locus_4sp_4.fasta,6,NaN,4,4,5,NaN +locus_4sp_6.fasta,6,7,6,7,NaN,NaN +locus_6sp_41.fasta,3,3,3,3,3,3 +locus_6sp_27.fasta,5,5,4,5,5,5 +locus_6sp_39.fasta,7,8,6,7,7,6 +locus_6sp_10.fasta,3,3,3,3,3,3 +locus_6sp_25.fasta,21,21,21,20,21,19 +locus_6sp_32.fasta,5,4,6,4,4,5 +locus_6sp_53.fasta,7,7,8,8,7,6 +locus_3sp_2.fasta,NaN,1,NaN,1,1,NaN +locus_6sp_47.fasta,6,6,6,6,6,6 +locus_6sp_16.fasta,2,2,3,2,2,3 +locus_6sp_11.fasta,9,9,9,8,8,9 +locus_6sp_35.fasta,2,2,2,2,2,3 +locus_6sp_46.fasta,6,5,6,8,8,7 +locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN +locus_6sp_30.fasta,0,0,0,0,0,0 +locus_6sp_57.fasta,5,5,5,5,5,5 +locus_6sp_50.fasta,7,7,7,7,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/RHK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,1,1,1,1,1,1 +locus_6sp_60.fasta,3,3,3,4,3,3 +locus_6sp_40.fasta,18,18,17,18,17,18 +locus_6sp_58.fasta,10,10,10,10,10,10 +locus_6sp_38.fasta,42,42,42,42,42,43 +locus_4sp_4.fasta,12,NaN,10,9,11,NaN +locus_4sp_6.fasta,17,17,18,18,NaN,NaN +locus_6sp_41.fasta,8,8,10,9,5,6 +locus_6sp_27.fasta,5,4,6,6,4,6 +locus_6sp_39.fasta,9,9,11,10,9,11 +locus_6sp_10.fasta,5,5,5,5,5,5 +locus_6sp_25.fasta,40,40,44,41,42,42 +locus_6sp_32.fasta,27,28,27,27,26,26 +locus_6sp_53.fasta,21,21,22,20,20,18 +locus_3sp_2.fasta,NaN,5,NaN,5,5,NaN +locus_6sp_47.fasta,23,23,23,23,23,23 +locus_6sp_16.fasta,3,3,3,3,3,3 +locus_6sp_11.fasta,22,23,23,24,23,22 +locus_6sp_35.fasta,6,6,8,7,7,7 +locus_6sp_46.fasta,37,39,39,38,38,39 +locus_3sp_7.fasta,5,5,5,NaN,NaN,NaN +locus_6sp_30.fasta,5,5,5,5,4,5 +locus_6sp_57.fasta,11,11,12,12,11,12 +locus_6sp_50.fasta,20,19,19,20,19,19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/RHKDE.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,3,3,3,3,3,3 +locus_6sp_60.fasta,7,7,7,8,7,7 +locus_6sp_40.fasta,31,31,30,30,30,30 +locus_6sp_58.fasta,13,13,13,13,13,13 +locus_6sp_38.fasta,54,54,54,54,54,55 +locus_4sp_4.fasta,14,NaN,13,11,14,NaN +locus_4sp_6.fasta,31,31,32,32,NaN,NaN +locus_6sp_41.fasta,11,11,13,12,8,9 +locus_6sp_27.fasta,6,5,9,7,5,7 +locus_6sp_39.fasta,16,15,18,16,15,18 +locus_6sp_10.fasta,9,9,9,9,9,9 +locus_6sp_25.fasta,81,81,86,81,81,84 +locus_6sp_32.fasta,46,47,46,48,45,45 +locus_6sp_53.fasta,38,38,39,36,35,35 +locus_3sp_2.fasta,NaN,10,NaN,10,9,NaN +locus_6sp_47.fasta,29,29,29,29,29,29 +locus_6sp_16.fasta,12,12,11,11,14,11 +locus_6sp_11.fasta,44,45,45,46,44,43 +locus_6sp_35.fasta,8,8,10,9,9,9 +locus_6sp_46.fasta,63,65,66,64,64,65 +locus_3sp_7.fasta,12,12,12,NaN,NaN,NaN +locus_6sp_30.fasta,8,8,8,8,8,8 +locus_6sp_57.fasta,23,23,24,24,23,24 +locus_6sp_50.fasta,31,30,29,31,30,29
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/STNQ.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2,2,2,2,2,2 +locus_6sp_60.fasta,7,7,8,7,7,8 +locus_6sp_40.fasta,13,13,12,12,13,11 +locus_6sp_58.fasta,35,35,36,36,36,36 +locus_6sp_38.fasta,33,34,33,34,34,32 +locus_4sp_4.fasta,15,NaN,14,18,10,NaN +locus_4sp_6.fasta,16,14,13,14,NaN,NaN +locus_6sp_41.fasta,23,23,21,22,23,23 +locus_6sp_27.fasta,5,5,4,7,5,5 +locus_6sp_39.fasta,10,12,8,12,10,8 +locus_6sp_10.fasta,10,10,10,10,10,10 +locus_6sp_25.fasta,57,59,54,57,57,53 +locus_6sp_32.fasta,20,19,20,20,18,20 +locus_6sp_53.fasta,21,22,21,23,23,22 +locus_3sp_2.fasta,NaN,4,NaN,4,3,NaN +locus_6sp_47.fasta,12,11,12,12,11,12 +locus_6sp_16.fasta,6,6,8,7,5,8 +locus_6sp_11.fasta,22,21,22,22,26,24 +locus_6sp_35.fasta,11,11,9,10,14,9 +locus_6sp_46.fasta,17,16,14,18,20,17 +locus_3sp_7.fasta,10,10,10,NaN,NaN,NaN +locus_6sp_30.fasta,2,2,2,2,2,2 +locus_6sp_57.fasta,21,21,21,22,21,20 +locus_6sp_50.fasta,38,39,39,36,38,39
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/VLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,9,8,8,8,8,8 +locus_6sp_60.fasta,4,4,3,2,4,3 +locus_6sp_40.fasta,26,27,28,29,27,28 +locus_6sp_58.fasta,1,1,1,0,0,1 +locus_6sp_38.fasta,1,1,1,1,3,3 +locus_4sp_4.fasta,26,NaN,25,23,27,NaN +locus_4sp_6.fasta,14,15,15,15,NaN,NaN +locus_6sp_41.fasta,19,19,19,18,20,20 +locus_6sp_27.fasta,14,14,13,15,16,13 +locus_6sp_39.fasta,10,9,10,9,12,10 +locus_6sp_10.fasta,14,14,14,14,15,14 +locus_6sp_25.fasta,71,71,69,71,73,73 +locus_6sp_32.fasta,33,33,31,31,33,31 +locus_6sp_53.fasta,21,21,21,23,22,25 +locus_3sp_2.fasta,NaN,5,NaN,5,6,NaN +locus_6sp_47.fasta,14,15,14,14,14,14 +locus_6sp_16.fasta,10,11,10,10,9,10 +locus_6sp_11.fasta,37,37,38,38,33,37 +locus_6sp_35.fasta,23,23,24,24,22,22 +locus_6sp_46.fasta,32,32,33,33,32,31 +locus_3sp_7.fasta,9,9,9,NaN,NaN,NaN +locus_6sp_30.fasta,3,3,3,3,3,3 +locus_6sp_57.fasta,25,25,25,25,26,25 +locus_6sp_50.fasta,89,90,89,90,89,89
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_AC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.111111111111,0.25,0.25,0.25,0.25,0.25 +locus_6sp_60.fasta,0.75,0.75,1.0,1.5,0.75,1.0 +locus_6sp_40.fasta,0.307692307692,0.259259259259,0.285714285714,0.206896551724,0.296296296296,0.285714285714 +locus_6sp_58.fasta,1.0,1.0,0.0,-1,-1,0.0 +locus_6sp_38.fasta,4.0,4.0,5.0,4.0,0.666666666667,1.0 +locus_4sp_4.fasta,0.230769230769,NaN,0.28,0.260869565217,0.259259259259,NaN +locus_4sp_6.fasta,0.928571428571,0.933333333333,0.866666666667,0.866666666667,NaN,NaN +locus_6sp_41.fasta,0.368421052632,0.368421052632,0.368421052632,0.388888888889,0.4,0.35 +locus_6sp_27.fasta,0.142857142857,0.214285714286,0.230769230769,0.133333333333,0.125,0.153846153846 +locus_6sp_39.fasta,0.3,0.333333333333,0.4,0.333333333333,0.25,0.4 +locus_6sp_10.fasta,0.571428571429,0.571428571429,0.571428571429,0.571428571429,0.466666666667,0.571428571429 +locus_6sp_25.fasta,0.281690140845,0.267605633803,0.304347826087,0.253521126761,0.27397260274,0.260273972603 +locus_6sp_32.fasta,0.272727272727,0.272727272727,0.354838709677,0.290322580645,0.272727272727,0.354838709677 +locus_6sp_53.fasta,0.333333333333,0.285714285714,0.285714285714,0.260869565217,0.272727272727,0.32 +locus_3sp_2.fasta,NaN,0.6,NaN,0.6,0.666666666667,NaN +locus_6sp_47.fasta,0.0714285714286,0.0666666666667,0.0714285714286,0.0714285714286,0.0714285714286,0.0714285714286 +locus_6sp_16.fasta,0.5,0.363636363636,0.4,0.4,0.555555555556,0.4 +locus_6sp_11.fasta,0.432432432432,0.432432432432,0.368421052632,0.394736842105,0.454545454545,0.405405405405 +locus_6sp_35.fasta,0.347826086957,0.347826086957,0.25,0.291666666667,0.272727272727,0.318181818182 +locus_6sp_46.fasta,0.21875,0.21875,0.212121212121,0.181818181818,0.15625,0.258064516129 +locus_3sp_7.fasta,0.333333333333,0.333333333333,0.333333333333,NaN,NaN,NaN +locus_6sp_30.fasta,0.333333333333,0.333333333333,0.333333333333,0.333333333333,0.333333333333,0.333333333333 +locus_6sp_57.fasta,0.4,0.4,0.36,0.32,0.346153846154,0.4 +locus_6sp_50.fasta,0.426966292135,0.411111111111,0.426966292135,0.444444444444,0.438202247191,0.438202247191
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_APGC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.555555555556,0.75,0.75,0.75,0.75,0.75 +locus_6sp_60.fasta,1.5,1.5,2.0,3.5,1.5,2.0 +locus_6sp_40.fasta,0.807692307692,0.740740740741,0.75,0.689655172414,0.777777777778,0.785714285714 +locus_6sp_58.fasta,5.0,5.0,4.0,-1,-1,4.0 +locus_6sp_38.fasta,15.0,14.0,15.0,14.0,4.0,4.33333333333 +locus_4sp_4.fasta,0.384615384615,NaN,0.44,0.434782608696,0.444444444444,NaN +locus_4sp_6.fasta,1.64285714286,1.6,1.53333333333,1.53333333333,NaN,NaN +locus_6sp_41.fasta,0.578947368421,0.578947368421,0.578947368421,0.611111111111,0.6,0.55 +locus_6sp_27.fasta,0.285714285714,0.357142857143,0.384615384615,0.133333333333,0.1875,0.384615384615 +locus_6sp_39.fasta,0.7,0.777777777778,0.8,0.777777777778,0.666666666667,0.8 +locus_6sp_10.fasta,1.0,1.0,1.0,1.0,0.866666666667,1.0 +locus_6sp_25.fasta,0.845070422535,0.816901408451,0.869565217391,0.816901408451,0.780821917808,0.794520547945 +locus_6sp_32.fasta,0.575757575758,0.575757575758,0.677419354839,0.612903225806,0.636363636364,0.677419354839 +locus_6sp_53.fasta,1.04761904762,1.0,1.0,0.913043478261,1.0,0.88 +locus_3sp_2.fasta,NaN,1.6,NaN,1.6,1.5,NaN +locus_6sp_47.fasta,0.571428571429,0.533333333333,0.571428571429,0.571428571429,0.642857142857,0.571428571429 +locus_6sp_16.fasta,1.1,0.909090909091,1.0,1.0,1.22222222222,1.0 +locus_6sp_11.fasta,1.0,1.0,0.921052631579,0.894736842105,1.09090909091,0.972972972973 +locus_6sp_35.fasta,0.739130434783,0.739130434783,0.583333333333,0.708333333333,0.636363636364,0.727272727273 +locus_6sp_46.fasta,0.40625,0.40625,0.393939393939,0.333333333333,0.3125,0.41935483871 +locus_3sp_7.fasta,0.333333333333,0.333333333333,0.333333333333,NaN,NaN,NaN +locus_6sp_30.fasta,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.666666666667 +locus_6sp_57.fasta,0.8,0.8,0.76,0.72,0.730769230769,0.8 +locus_6sp_50.fasta,1.01123595506,0.988888888889,1.01123595506,1.02222222222,1.03370786517,1.02247191011
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_EK_QH.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2.0,2.0,2.0,2.0,2.0,2.0 +locus_6sp_60.fasta,-1,-1,-1,-1,-1,-1 +locus_6sp_40.fasta,4.0,4.0,4.75,4.5,4.0,4.75 +locus_6sp_58.fasta,1.0,1.0,1.0,0.5,1.0,1.0 +locus_6sp_38.fasta,1.69230769231,1.69230769231,1.91666666667,1.75,2.1,2.0 +locus_4sp_4.fasta,0.333333333333,NaN,0.5,0.5,0.2,NaN +locus_4sp_6.fasta,2.0,1.71428571429,2.66666666667,1.85714285714,NaN,NaN +locus_6sp_41.fasta,0.666666666667,1.0,0.666666666667,0.666666666667,0.666666666667,0.666666666667 +locus_6sp_27.fasta,0.2,0.2,0.5,0.2,0.2,0.2 +locus_6sp_39.fasta,1.28571428571,0.875,1.33333333333,1.0,1.14285714286,1.33333333333 +locus_6sp_10.fasta,1.33333333333,1.33333333333,1.33333333333,1.33333333333,1.33333333333,1.33333333333 +locus_6sp_25.fasta,1.71428571429,1.66666666667,1.85714285714,1.85,1.80952380952,1.94736842105 +locus_6sp_32.fasta,6.2,8.0,5.33333333333,8.5,7.75,6.6 +locus_6sp_53.fasta,3.42857142857,3.42857142857,2.875,2.875,3.28571428571,3.66666666667 +locus_3sp_2.fasta,NaN,5.0,NaN,6.0,5.0,NaN +locus_6sp_47.fasta,2.0,2.0,2.0,2.0,2.0,2.0 +locus_6sp_16.fasta,4.0,4.0,2.33333333333,4.0,4.0,2.33333333333 +locus_6sp_11.fasta,3.22222222222,3.22222222222,3.11111111111,3.625,3.5,3.11111111111 +locus_6sp_35.fasta,1.5,1.5,1.5,1.5,1.5,1.0 +locus_6sp_46.fasta,7.5,9.2,8.16666666667,5.5,6.0,6.71428571429 +locus_3sp_7.fasta,1.4,1.2,1.4,NaN,NaN,NaN +locus_6sp_30.fasta,-1,-1,-1,-1,-1,-1 +locus_6sp_57.fasta,2.6,2.6,2.4,2.6,2.4,2.6 +locus_6sp_50.fasta,1.57142857143,1.14285714286,1.28571428571,1.42857142857,1.125,1.28571428571
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_ERK_DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.5,0.4,0.4,0.4,0.4,0.4 +locus_6sp_60.fasta,0.363636363636,0.363636363636,0.166666666667,0.25,0.363636363636,0.166666666667 +locus_6sp_40.fasta,0.862068965517,0.888888888889,1.16,1.12,0.862068965517,1.20833333333 +locus_6sp_58.fasta,0.05,0.05,0.05,0.0487804878049,0.0487804878049,0.05 +locus_6sp_38.fasta,0.698113207547,0.685185185185,0.730769230769,0.666666666667,0.72,0.74 +locus_4sp_4.fasta,0.12,NaN,0.136363636364,0.12,0.0526315789474,NaN +locus_4sp_6.fasta,0.68,0.68,1.14285714286,0.791666666667,NaN,NaN +locus_6sp_41.fasta,0.0967741935484,0.161290322581,0.103448275862,0.1,0.0967741935484,0.0967741935484 +locus_6sp_27.fasta,0.2,0.2,0.222222222222,0.181818181818,0.125,0.222222222222 +locus_6sp_39.fasta,0.684210526316,0.47619047619,0.611111111111,0.47619047619,0.666666666667,0.611111111111 +locus_6sp_10.fasta,0.315789473684,0.315789473684,0.315789473684,0.315789473684,0.333333333333,0.315789473684 +locus_6sp_25.fasta,0.495412844037,0.472727272727,0.546296296296,0.532710280374,0.546296296296,0.528301886792 +locus_6sp_32.fasta,1.38888888889,1.48571428571,1.34210526316,1.47222222222,1.47058823529,1.44444444444 +locus_6sp_53.fasta,1.0,1.0,0.916666666667,0.942857142857,0.971428571429,0.914285714286 +locus_3sp_2.fasta,NaN,0.818181818182,NaN,1.0,0.9,NaN +locus_6sp_47.fasta,1.1,1.15789473684,1.1,1.1,1.15789473684,1.1 +locus_6sp_16.fasta,0.714285714286,0.769230769231,0.6,0.769230769231,0.666666666667,0.6 +locus_6sp_11.fasta,1.0,1.0,0.977272727273,1.0,0.895833333333,0.955555555556 +locus_6sp_35.fasta,0.294117647059,0.294117647059,0.3125,0.3125,0.25,0.3125 +locus_6sp_46.fasta,2.42857142857,2.59259259259,3.08333333333,2.35714285714,2.55172413793,2.53571428571 +locus_3sp_7.fasta,0.647058823529,0.555555555556,0.647058823529,NaN,NaN,NaN +locus_6sp_30.fasta,2.5,2.5,2.5,2.5,2.25,2.0 +locus_6sp_57.fasta,0.5,0.5,0.472222222222,0.514285714286,0.472222222222,0.514285714286 +locus_6sp_50.fasta,0.219512195122,0.156626506024,0.180722891566,0.192771084337,0.176470588235,0.178571428571
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/ratio_GARP_FYMINK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,0.285714285714,0.285714285714,0.333333333333,0.285714285714,0.285714285714,0.285714285714 +locus_6sp_60.fasta,0.5,0.5,0.333333333333,0.285714285714,0.5,0.333333333333 +locus_6sp_40.fasta,0.571428571429,0.615384615385,0.678571428571,0.666666666667,0.592592592593,0.678571428571 +locus_6sp_58.fasta,0.333333333333,0.333333333333,0.5,0.5,0.333333333333,0.5 +locus_6sp_38.fasta,0.666666666667,0.666666666667,0.69696969697,0.636363636364,0.617647058824,0.666666666667 +locus_4sp_4.fasta,0.111111111111,NaN,0.0909090909091,0.0833333333333,0.0416666666667,NaN +locus_4sp_6.fasta,0.461538461538,0.461538461538,0.571428571429,0.52,NaN,NaN +locus_6sp_41.fasta,0.133333333333,0.2,0.142857142857,0.133333333333,0.133333333333,0.125 +locus_6sp_27.fasta,0.25,0.25,1.0,0.25,0.166666666667,0.2 +locus_6sp_39.fasta,0.5,0.4375,0.470588235294,0.411764705882,0.5,0.470588235294 +locus_6sp_10.fasta,0.16,0.16,0.166666666667,0.16,0.166666666667,0.166666666667 +locus_6sp_25.fasta,0.439024390244,0.426829268293,0.493670886076,0.456790123457,0.436781609195,0.46835443038 +locus_6sp_32.fasta,0.659574468085,0.68085106383,0.727272727273,0.755555555556,0.673913043478,0.733333333333 +locus_6sp_53.fasta,0.615384615385,0.615384615385,0.638888888889,0.621621621622,0.638888888889,0.578947368421 +locus_3sp_2.fasta,NaN,0.555555555556,NaN,0.6,0.555555555556,NaN +locus_6sp_47.fasta,0.75,0.705882352941,0.75,0.75,0.75,0.75 +locus_6sp_16.fasta,1.0,1.0,0.777777777778,0.727272727273,0.888888888889,0.875 +locus_6sp_11.fasta,0.644444444444,0.644444444444,0.595744680851,0.644444444444,0.622222222222,0.608695652174 +locus_6sp_35.fasta,0.15,0.142857142857,0.142857142857,0.136363636364,0.130434782609,0.130434782609 +locus_6sp_46.fasta,0.918367346939,0.938775510204,1.0,0.95652173913,0.941176470588,0.979166666667 +locus_3sp_7.fasta,0.875,0.75,0.875,NaN,NaN,NaN +locus_6sp_30.fasta,0.666666666667,0.666666666667,0.666666666667,0.666666666667,0.75,0.625 +locus_6sp_57.fasta,0.722222222222,0.722222222222,0.631578947368,0.684210526316,0.631578947368,0.684210526316 +locus_6sp_50.fasta,0.142857142857,0.108108108108,0.1125,0.133333333333,0.118421052632,0.1125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_hydration.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,45.0,45.0,45.0,45.0,45.0,45.0 +locus_6sp_60.fasta,61.5,61.5,61.0,62.0,61.5,61.0 +locus_6sp_40.fasta,247.0,247.0,246.5,245.0,245.0,245.5 +locus_6sp_58.fasta,126.5,126.5,127.5,130.5,127.5,127.5 +locus_6sp_38.fasta,376.0,375.0,374.5,372.5,367.5,374.0 +locus_4sp_4.fasta,135.0,NaN,134.0,129.0,130.5,NaN +locus_4sp_6.fasta,257.0,256.0,264.0,262.5,NaN,NaN +locus_6sp_41.fasta,126.0,127.5,128.0,126.0,118.0,121.0 +locus_6sp_27.fasta,57.5,55.5,74.0,61.5,55.5,62.5 +locus_6sp_39.fasta,138.5,129.5,135.0,130.5,130.0,135.0 +locus_6sp_10.fasta,125.0,125.0,125.0,125.0,122.0,125.0 +locus_6sp_25.fasta,747.0,745.5,758.5,744.5,742.0,749.5 +locus_6sp_32.fasta,359.5,362.0,359.0,372.0,356.5,359.5 +locus_6sp_53.fasta,317.0,318.0,319.5,311.5,305.5,307.0 +locus_3sp_2.fasta,NaN,85.5,NaN,87.0,79.5,NaN +locus_6sp_47.fasta,180.0,179.0,180.0,180.0,179.0,180.0 +locus_6sp_16.fasta,114.0,114.0,112.5,112.0,123.0,112.5 +locus_6sp_11.fasta,378.5,380.5,380.0,384.5,378.0,374.0 +locus_6sp_35.fasta,118.5,118.5,119.5,121.5,121.5,114.5 +locus_6sp_46.fasta,429.5,435.0,442.5,432.0,440.0,437.5 +locus_3sp_7.fasta,102.5,101.0,102.5,NaN,NaN,NaN +locus_6sp_30.fasta,57.0,57.0,57.0,57.0,60.0,55.5 +locus_6sp_57.fasta,226.5,226.5,224.0,226.5,225.0,224.5 +locus_6sp_50.fasta,473.5,468.0,463.5,469.0,467.5,464.5
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_partial_specific_volume.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,15.64,15.52,15.67,15.52,15.48,15.52 +locus_6sp_60.fasta,19.64,19.64,19.24,19.04,19.64,19.24 +locus_6sp_40.fasta,71.19,71.17,71.58,71.77,71.43,71.62 +locus_6sp_58.fasta,38.79,38.83,38.79,38.62,38.55,38.79 +locus_6sp_38.fasta,81.92,81.86,82.03,81.87,82.29,82.24 +locus_4sp_4.fasta,55.12,NaN,54.64,54.51,54.66,NaN +locus_4sp_6.fasta,67.26,67.51,67.91,67.51,NaN,NaN +locus_6sp_41.fasta,51.81,52.05,51.85,51.91,52.2,52.23 +locus_6sp_27.fasta,25.85,25.76,25.41,25.71,26.01,25.59 +locus_6sp_39.fasta,38.27,38.12,38.34,38.04,38.67,38.34 +locus_6sp_10.fasta,45.83,45.83,45.98,45.83,46.26,45.98 +locus_6sp_25.fasta,219.26,218.84,219.08,219.6,219.52,219.72 +locus_6sp_32.fasta,98.84,98.99,98.67,98.57,98.6,98.67 +locus_6sp_53.fasta,87.81,87.77,87.58,88.01,88.13,87.94 +locus_3sp_2.fasta,NaN,23.01,NaN,23.11,23.31,NaN +locus_6sp_47.fasta,48.9,48.95,48.9,48.9,48.8,48.9 +locus_6sp_16.fasta,30.88,31.0,30.61,30.81,30.52,30.69 +locus_6sp_11.fasta,110.48,110.63,110.48,110.41,110.02,110.42 +locus_6sp_35.fasta,54.48,54.52,55.0,54.63,54.6,54.4 +locus_6sp_46.fasta,103.31,103.35,103.88,103.24,103.59,103.44 +locus_3sp_7.fasta,25.94,25.88,25.9,NaN,NaN,NaN +locus_6sp_30.fasta,13.25,13.25,13.25,13.25,13.09,13.13 +locus_6sp_57.fasta,68.74,68.74,68.68,68.74,68.88,68.78 +locus_6sp_50.fasta,205.01,204.83,204.81,204.76,204.37,204.67
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_residue_volume.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2202.0,2164.0,2164.0,2164.0,2145.0,2164.0 +locus_6sp_60.fasta,2631.0,2631.0,2616.0,2603.0,2631.0,2616.0 +locus_6sp_40.fasta,10101.0,10132.0,10106.0,10120.0,10094.0,10093.0 +locus_6sp_58.fasta,4711.0,4691.0,4678.0,4653.0,4663.0,4678.0 +locus_6sp_38.fasta,12698.0,12701.0,12664.0,12654.0,12843.0,12756.0 +locus_4sp_4.fasta,7925.0,NaN,8022.0,7964.0,8152.0,NaN +locus_4sp_6.fasta,10595.0,10587.0,10722.0,10619.0,NaN,NaN +locus_6sp_41.fasta,7107.0,7071.0,7234.0,7170.0,7037.0,7070.0 +locus_6sp_27.fasta,3695.0,3633.0,3713.0,3763.0,3851.0,3731.0 +locus_6sp_39.fasta,5787.0,5768.0,5787.0,5731.0,5749.0,5787.0 +locus_6sp_10.fasta,6919.0,6919.0,6919.0,6919.0,6951.0,6919.0 +locus_6sp_25.fasta,31048.0,31038.0,31072.0,31049.0,31208.0,31071.0 +locus_6sp_32.fasta,14655.0,14676.0,14543.0,14585.0,14554.0,14584.0 +locus_6sp_53.fasta,12891.0,12917.0,12885.0,12899.0,12753.0,12841.0 +locus_3sp_2.fasta,NaN,3365.0,NaN,3402.0,3353.0,NaN +locus_6sp_47.fasta,7357.0,7388.0,7357.0,7357.0,7332.0,7357.0 +locus_6sp_16.fasta,4093.0,4131.0,4133.0,4191.0,4116.0,4130.0 +locus_6sp_11.fasta,15542.0,15546.0,15644.0,15666.0,15488.0,15585.0 +locus_6sp_35.fasta,7718.0,7737.0,7901.0,7679.0,7737.0,7819.0 +locus_6sp_46.fasta,16044.0,16059.0,16094.0,16156.0,16121.0,16087.0 +locus_3sp_7.fasta,3822.0,3804.0,3842.0,NaN,NaN,NaN +locus_6sp_30.fasta,2160.0,2160.0,2160.0,2160.0,2134.0,2173.0 +locus_6sp_57.fasta,9302.0,9302.0,9382.0,9406.0,9321.0,9374.0 +locus_6sp_50.fasta,27199.0,27151.0,27205.0,27077.0,26938.0,27156.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/02_tables_per_aa_variable/total_residue_weight.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Ac,Ap,Pf,Pg,Pp,Ps +locus_6sp_18.fasta,2320.97,2292.91,2274.88,2292.91,2278.88,2292.91 +locus_6sp_60.fasta,2875.44,2875.44,2904.37,2890.36,2875.44,2904.37 +locus_6sp_40.fasta,10730.6,10772.64,10677.71,10681.73,10687.63,10669.73 +locus_6sp_58.fasta,5382.96,5368.93,5370.9,5363.87,5369.85,5370.9 +locus_6sp_38.fasta,14051.67,14055.66,14016.61,14018.58,14138.94,14087.76 +locus_4sp_4.fasta,8273.9,NaN,8399.0,8384.92,8550.4,NaN +locus_4sp_6.fasta,11670.96,11635.0,11719.17,11667.99,NaN,NaN +locus_6sp_41.fasta,7552.64,7497.62,7665.85,7611.72,7445.58,7480.58 +locus_6sp_27.fasta,3817.14,3763.09,3880.11,3891.27,3935.29,3871.22 +locus_6sp_39.fasta,6222.42,6222.47,6204.5,6184.45,6113.49,6204.5 +locus_6sp_10.fasta,7526.22,7526.22,7508.19,7526.22,7520.32,7508.19 +locus_6sp_25.fasta,33249.0,33294.9,33269.07,33233.11,33387.33,33234.18 +locus_6sp_32.fasta,15445.36,15446.41,15354.27,15414.27,15382.32,15393.26 +locus_6sp_53.fasta,13805.76,13835.79,13840.75,13785.8,13638.67,13709.73 +locus_3sp_2.fasta,NaN,3643.31,NaN,3671.37,3598.35,NaN +locus_6sp_47.fasta,7739.7,7769.79,7739.7,7739.7,7709.68,7739.7 +locus_6sp_16.fasta,4402.26,4430.32,4461.23,4508.34,4458.21,4448.25 +locus_6sp_11.fasta,16434.68,16426.67,16557.81,16592.75,16450.49,16492.74 +locus_6sp_35.fasta,8146.67,8160.7,8310.84,8072.54,8176.59,8286.85 +locus_6sp_46.fasta,16798.11,16795.14,16783.11,16934.22,16849.13,16833.11 +locus_3sp_7.fasta,4052.77,4038.74,4066.8,NaN,NaN,NaN +locus_6sp_30.fasta,2321.9,2321.9,2321.9,2321.9,2320.82,2349.91 +locus_6sp_57.fasta,9928.19,9928.19,10011.35,10041.38,9942.22,9995.35 +locus_6sp_50.fasta,28621.97,28607.88,28658.02,28528.93,28444.68,28613.98
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/A.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,1,4,5 +"Lower",1,4,4,0 +"Difference",2,-3,0,5 +"Trial_Number",4,5,8,5 +"p-value",0.625,0.375,1,0.0625 +"probability_of_success",0.75,0.2,0.5,1 +"confidence_interval_low",0.194120449683243,0.00505076337946806,0.157012770487058,0.478176249895019 +"confidence_interval_high",0.99369053679029,0.716417936118089,0.842987229512942,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/C.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,0,0,2 +"Lower",0,0,2,0 +"Difference",1,0,-2,2 +"Trial_Number",1,0,2,2 +"p-value",1,NA,0.5,0.5 +"probability_of_success",1,NA,0,1 +"confidence_interval_low",0.025,NA,0,0.158113883008419 +"confidence_interval_high",1,NA,0.841886116991581,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/D.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,2,4,2 +"Lower",1,2,3,4 +"Difference",1,0,1,-2 +"Trial_Number",3,4,7,6 +"p-value",1,1,1,0.6875 +"probability_of_success",0.666666666666667,0.5,0.571428571428571,0.333333333333333 +"confidence_interval_low",0.0942993240502461,0.067585986488543,0.184051567640083,0.0432718682927417 +"confidence_interval_high",0.991596241340387,0.932414013511457,0.901011721557492,0.777221904496488
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/E.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,3,2,5 +"Lower",0,3,4,1 +"Difference",2,0,-2,4 +"Trial_Number",2,6,6,6 +"p-value",0.5,1,0.6875,0.21875 +"probability_of_success",1,0.5,0.333333333333333,0.833333333333333 +"confidence_interval_low",0.158113883008419,0.118117248757025,0.0432718682927417,0.358765421002325 +"confidence_interval_high",1,0.881882751242975,0.777221904496488,0.995789255485511
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/F.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,0,3,1 +"Lower",2,3,1,2 +"Difference",-1,-3,2,-1 +"Trial_Number",3,3,4,3 +"p-value",1,0.25,0.625,1 +"probability_of_success",0.333333333333333,0,0.75,0.333333333333333 +"confidence_interval_low",0.00840375865961264,0,0.194120449683243,0.00840375865961264 +"confidence_interval_high",0.905700675949754,0.707598226178713,0.99369053679029,0.905700675949754
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/G.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,5,0 +"Lower",0,2,1,0 +"Difference",1,-1,4,0 +"Trial_Number",1,3,6,0 +"p-value",1,1,0.21875,NA +"probability_of_success",1,0.333333333333333,0.833333333333333,NA +"confidence_interval_low",0.025,0.00840375865961264,0.358765421002325,NA +"confidence_interval_high",1,0.905700675949754,0.995789255485511,NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/H.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,3,1,2 +"Lower",1,0,4,3 +"Difference",0,3,-3,-1 +"Trial_Number",2,3,5,5 +"p-value",1,0.25,0.375,1 +"probability_of_success",0.5,1,0.2,0.4 +"confidence_interval_low",0.0125791170934251,0.292401773821287,0.00505076337946806,0.0527449505263169 +"confidence_interval_high",0.987420882906575,1,0.716417936118089,0.853367200365327
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/I.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,2,6,2 +"Lower",3,4,4,2 +"Difference",2,-2,2,0 +"Trial_Number",8,6,10,4 +"p-value",0.7265625,0.6875,0.75390625,1 +"probability_of_success",0.625,0.333333333333333,0.6,0.5 +"confidence_interval_low",0.244863216366552,0.0432718682927417,0.262378076606945,0.067585986488543 +"confidence_interval_high",0.914766585862746,0.777221904496488,0.878447741880173,0.932414013511457
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/K.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,1,3,0 +"Lower",3,1,1,2 +"Difference",0,0,2,-2 +"Trial_Number",6,2,4,2 +"p-value",1,1,0.625,0.5 +"probability_of_success",0.5,0.5,0.75,0 +"confidence_interval_low",0.118117248757025,0.0125791170934251,0.194120449683243,0 +"confidence_interval_high",0.881882751242975,0.987420882906575,0.99369053679029,0.841886116991581
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/L.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,2,3,3 +"Lower",3,3,2,2 +"Difference",-1,-1,1,1 +"Trial_Number",5,5,5,5 +"p-value",1,1,1,1 +"probability_of_success",0.4,0.4,0.6,0.6 +"confidence_interval_low",0.0527449505263169,0.0527449505263169,0.146632799634673,0.146632799634673 +"confidence_interval_high",0.853367200365327,0.853367200365327,0.947255049473683,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/M.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,2,2,2 +"Lower",2,0,1,0 +"Difference",-1,2,1,2 +"Trial_Number",3,2,3,2 +"p-value",1,0.5,1,0.5 +"probability_of_success",0.333333333333333,1,0.666666666666667,1 +"confidence_interval_low",0.00840375865961264,0.158113883008419,0.0942993240502461,0.158113883008419 +"confidence_interval_high",0.905700675949754,1,0.991596241340387,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/N.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,4,2 +"Lower",2,0,2,0 +"Difference",-1,1,2,2 +"Trial_Number",3,1,6,2 +"p-value",1,1,0.6875,0.5 +"probability_of_success",0.333333333333333,1,0.666666666666667,1 +"confidence_interval_low",0.00840375865961264,0.025,0.222778095503512,0.158113883008419 +"confidence_interval_high",0.905700675949754,1,0.956728131707258,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/P.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,1,1 +"Lower",0,2,1,1 +"Difference",1,-1,0,0 +"Trial_Number",1,3,2,2 +"p-value",1,1,1,1 +"probability_of_success",1,0.333333333333333,0.5,0.5 +"confidence_interval_low",0.025,0.00840375865961264,0.0125791170934251,0.0125791170934251 +"confidence_interval_high",1,0.905700675949754,0.987420882906575,0.987420882906575
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/Q.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,1,3,3 +"Lower",1,3,1,4 +"Difference",0,-2,2,-1 +"Trial_Number",2,4,4,7 +"p-value",1,0.625,0.625,1 +"probability_of_success",0.5,0.25,0.75,0.428571428571429 +"confidence_interval_low",0.0125791170934251,0.00630946320970987,0.194120449683243,0.0989882784425079 +"confidence_interval_high",0.987420882906575,0.805879550316757,0.99369053679029,0.815948432359917
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/R.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,4,2,3 +"Lower",4,2,4,1 +"Difference",0,2,-2,2 +"Trial_Number",8,6,6,4 +"p-value",1,0.6875,0.6875,0.625 +"probability_of_success",0.5,0.666666666666667,0.333333333333333,0.75 +"confidence_interval_low",0.157012770487058,0.222778095503512,0.0432718682927417,0.194120449683243 +"confidence_interval_high",0.842987229512942,0.956728131707258,0.777221904496488,0.99369053679029
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/S.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,5,4,1 +"Lower",3,2,3,3 +"Difference",-1,3,1,-2 +"Trial_Number",5,7,7,4 +"p-value",1,0.453125,1,0.625 +"probability_of_success",0.4,0.714285714285714,0.571428571428571,0.25 +"confidence_interval_low",0.0527449505263169,0.290420863737343,0.184051567640083,0.00630946320970987 +"confidence_interval_high",0.853367200365327,0.963307433823914,0.901011721557492,0.805879550316757
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/T.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,4,2,2 +"Lower",2,2,2,3 +"Difference",0,2,0,-1 +"Trial_Number",4,6,4,5 +"p-value",1,0.6875,1,1 +"probability_of_success",0.5,0.666666666666667,0.5,0.4 +"confidence_interval_low",0.067585986488543,0.222778095503512,0.067585986488543,0.0527449505263169 +"confidence_interval_high",0.932414013511457,0.956728131707258,0.932414013511457,0.853367200365327
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/V.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,4,4,3 +"Lower",2,4,4,2 +"Difference",0,0,0,1 +"Trial_Number",4,8,8,5 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.5,0.5,0.6 +"confidence_interval_low",0.067585986488543,0.157012770487058,0.157012770487058,0.146632799634673 +"confidence_interval_high",0.932414013511457,0.842987229512942,0.842987229512942,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/W.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",0,0,0,0 +"Lower",0,1,0,0 +"Difference",0,-1,0,0 +"Trial_Number",0,1,0,0 +"p-value",NA,1,NA,NA +"probability_of_success",NA,0,NA,NA +"confidence_interval_low",NA,0,NA,NA +"confidence_interval_high",NA,0.975,NA,NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa/Y.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,3,2,1 +"Lower",1,2,3,1 +"Difference",0,1,-1,0 +"Trial_Number",2,5,5,2 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.6,0.4,0.5 +"confidence_interval_low",0.0125791170934251,0.146632799634673,0.0527449505263169,0.0125791170934251 +"confidence_interval_high",0.987420882906575,0.947255049473683,0.853367200365327,0.987420882906575
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/AC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,1,3,5 +"Lower",1,4,5,0 +"Difference",4,-3,-2,5 +"Trial_Number",6,5,8,5 +"p-value",0.21875,0.375,0.7265625,0.0625 +"probability_of_success",0.833333333333333,0.2,0.375,1 +"confidence_interval_low",0.358765421002325,0.00505076337946806,0.0852334141372536,0.478176249895019 +"confidence_interval_high",0.995789255485511,0.716417936118089,0.755136783633448,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/APGC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,2,4,4 +"Lower",1,4,7,2 +"Difference",3,-2,-3,2 +"Trial_Number",5,6,11,6 +"p-value",0.375,0.6875,0.548828125,0.6875 +"probability_of_success",0.8,0.333333333333333,0.363636363636364,0.666666666666667 +"confidence_interval_low",0.283582063881911,0.0432718682927417,0.109263443819098,0.222778095503512 +"confidence_interval_high",0.994949236620532,0.777221904496488,0.692095284988323,0.956728131707258
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/AVLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,2,4,2 +"Lower",3,6,2,1 +"Difference",0,-4,2,1 +"Trial_Number",6,8,6,3 +"p-value",1,0.2890625,0.6875,1 +"probability_of_success",0.5,0.25,0.666666666666667,0.666666666666667 +"confidence_interval_low",0.118117248757025,0.0318540262499442,0.222778095503512,0.0942993240502461 +"confidence_interval_high",0.881882751242975,0.650855794412824,0.956728131707258,0.991596241340387
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/AVLIMFYW.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,1,3,3 +"Lower",3,5,3,1 +"Difference",-1,-4,0,2 +"Trial_Number",5,6,6,4 +"p-value",1,0.21875,1,0.625 +"probability_of_success",0.4,0.166666666666667,0.5,0.75 +"confidence_interval_low",0.0527449505263169,0.00421074451448947,0.118117248757025,0.194120449683243 +"confidence_interval_high",0.853367200365327,0.641234578997675,0.881882751242975,0.99369053679029
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/DE.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,1,2,3 +"Lower",0,2,2,1 +"Difference",2,-1,0,2 +"Trial_Number",2,3,4,4 +"p-value",0.5,1,1,0.625 +"probability_of_success",1,0.333333333333333,0.5,0.75 +"confidence_interval_low",0.158113883008419,0.00840375865961264,0.067585986488543,0.194120449683243 +"confidence_interval_high",1,0.905700675949754,0.932414013511457,0.99369053679029
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",1,2,6,0 +"Lower",2,2,3,3 +"Difference",-1,0,3,-3 +"Trial_Number",3,4,9,3 +"p-value",1,1,0.5078125,0.25 +"probability_of_success",0.333333333333333,0.5,0.666666666666667,0 +"confidence_interval_low",0.00840375865961264,0.067585986488543,0.29929505620854,0 +"confidence_interval_high",0.905700675949754,0.932414013511457,0.925145368580308,0.707598226178713
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/EK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,2,2,2 +"Lower",2,2,3,3 +"Difference",1,0,-1,-1 +"Trial_Number",5,4,5,5 +"p-value",1,1,1,1 +"probability_of_success",0.6,0.5,0.4,0.4 +"confidence_interval_low",0.146632799634673,0.067585986488543,0.0527449505263169,0.0527449505263169 +"confidence_interval_high",0.947255049473683,0.932414013511457,0.853367200365327,0.853367200365327
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ERK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,3,3,2 +"Lower",3,2,4,5 +"Difference",1,1,-1,-3 +"Trial_Number",7,5,7,7 +"p-value",1,1,1,0.453125 +"probability_of_success",0.571428571428571,0.6,0.428571428571429,0.285714285714286 +"confidence_interval_low",0.184051567640083,0.146632799634673,0.0989882784425079,0.0366925661760856 +"confidence_interval_high",0.901011721557492,0.947255049473683,0.815948432359917,0.709579136262657
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/FYMINK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,2,5,5 +"Lower",5,2,1,2 +"Difference",-2,0,4,3 +"Trial_Number",8,4,6,7 +"p-value",0.7265625,1,0.21875,0.453125 +"probability_of_success",0.375,0.5,0.833333333333333,0.714285714285714 +"confidence_interval_low",0.0852334141372536,0.067585986488543,0.358765421002325,0.290420863737343 +"confidence_interval_high",0.755136783633448,0.932414013511457,0.995789255485511,0.963307433823914
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/FYW.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,2,1,2 +"Lower",2,3,2,1 +"Difference",0,-1,-1,1 +"Trial_Number",4,5,3,3 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.4,0.333333333333333,0.666666666666667 +"confidence_interval_low",0.067585986488543,0.0527449505263169,0.00840375865961264,0.0942993240502461 +"confidence_interval_high",0.932414013511457,0.853367200365327,0.905700675949754,0.991596241340387
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/GARP.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",4,4,2,6 +"Lower",3,7,4,1 +"Difference",1,-3,-2,5 +"Trial_Number",7,11,6,7 +"p-value",1,0.548828125,0.6875,0.125 +"probability_of_success",0.571428571428571,0.363636363636364,0.333333333333333,0.857142857142857 +"confidence_interval_low",0.184051567640083,0.109263443819098,0.0432718682927417,0.421276802956805 +"confidence_interval_high",0.901011721557492,0.692095284988323,0.777221904496488,0.996389703138099
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/IVYWREL.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,5,1,3 +"Lower",1,4,9,2 +"Difference",4,1,-8,1 +"Trial_Number",6,9,10,5 +"p-value",0.21875,1,0.021484375,1 +"probability_of_success",0.833333333333333,0.555555555555556,0.1,0.6 +"confidence_interval_low",0.358765421002325,0.212008506778868,0.00252857854446179,0.146632799634673 +"confidence_interval_high",0.995789255485511,0.863004337734833,0.445016117028195,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/QH.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,3,2,4 +"Lower",1,1,2,4 +"Difference",2,2,0,0 +"Trial_Number",4,4,4,8 +"p-value",0.625,0.625,1,1 +"probability_of_success",0.75,0.75,0.5,0.5 +"confidence_interval_low",0.194120449683243,0.194120449683243,0.067585986488543,0.157012770487058 +"confidence_interval_high",0.99369053679029,0.99369053679029,0.932414013511457,0.842987229512942
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/RHK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,4,0,3 +"Lower",2,1,4,2 +"Difference",1,3,-4,1 +"Trial_Number",5,5,4,5 +"p-value",1,0.375,0.125,1 +"probability_of_success",0.6,0.8,0,0.6 +"confidence_interval_low",0.146632799634673,0.283582063881911,0,0.146632799634673 +"confidence_interval_high",0.947255049473683,0.994949236620532,0.602364635616475,0.947255049473683
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/RHKDE.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,5,1,4 +"Lower",1,1,2,2 +"Difference",2,4,-1,2 +"Trial_Number",4,6,3,6 +"p-value",0.625,0.21875,1,0.6875 +"probability_of_success",0.75,0.833333333333333,0.333333333333333,0.666666666666667 +"confidence_interval_low",0.194120449683243,0.358765421002325,0.00840375865961264,0.222778095503512 +"confidence_interval_high",0.99369053679029,0.995789255485511,0.905700675949754,0.956728131707258
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/STNQ.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",2,4,4,3 +"Lower",4,2,3,8 +"Difference",-2,2,1,-5 +"Trial_Number",6,6,7,11 +"p-value",0.6875,0.6875,1,0.2265625 +"probability_of_success",0.333333333333333,0.666666666666667,0.571428571428571,0.272727272727273 +"confidence_interval_low",0.0432718682927417,0.222778095503512,0.184051567640083,0.0602177341729066 +"confidence_interval_high",0.777221904496488,0.956728131707258,0.901011721557492,0.609742559572421
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/VLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,5,4,2 +"Lower",2,3,3,2 +"Difference",1,2,1,0 +"Trial_Number",5,8,7,4 +"p-value",1,0.7265625,1,1 +"probability_of_success",0.6,0.625,0.571428571428571,0.5 +"confidence_interval_low",0.146632799634673,0.244863216366552,0.184051567640083,0.067585986488543 +"confidence_interval_high",0.947255049473683,0.914766585862746,0.901011721557492,0.932414013511457
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_AC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,3,5,8 +"Lower",4,9,9,1 +"Difference",2,-6,-4,7 +"Trial_Number",10,12,14,9 +"p-value",0.75390625,0.14599609375,0.4239501953125,0.0390625 +"probability_of_success",0.6,0.25,0.357142857142857,0.888888888888889 +"confidence_interval_low",0.262378076606945,0.0548606445279928,0.127598429859159,0.517503485082663 +"confidence_interval_high",0.878447741880173,0.571858461878189,0.648619889384008,0.997190863253401
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_APGC_VLIM.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,2,5,8 +"Lower",5,7,9,2 +"Difference",0,-5,-4,6 +"Trial_Number",10,9,14,10 +"p-value",1,0.1796875,0.4239501953125,0.109375 +"probability_of_success",0.5,0.222222222222222,0.357142857142857,0.8 +"confidence_interval_low",0.187086028447399,0.0281449734778982,0.127598429859159,0.443904537692359 +"confidence_interval_high",0.812913971552601,0.600093573716312,0.648619889384008,0.974789273673167
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_EK_QH.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",3,3,2,5 +"Lower",4,3,4,4 +"Difference",-1,0,-2,1 +"Trial_Number",7,6,6,9 +"p-value",1,1,0.6875,1 +"probability_of_success",0.428571428571429,0.5,0.333333333333333,0.555555555555556 +"confidence_interval_low",0.0989882784425079,0.118117248757025,0.0432718682927417,0.212008506778868 +"confidence_interval_high",0.815948432359917,0.881882751242975,0.777221904496488,0.863004337734833
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_ERK_DNQTSHA.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,2,3,4 +"Lower",2,4,6,6 +"Difference",4,-2,-3,-2 +"Trial_Number",8,6,9,10 +"p-value",0.2890625,0.6875,0.5078125,0.75390625 +"probability_of_success",0.75,0.333333333333333,0.333333333333333,0.4 +"confidence_interval_low",0.349144205587176,0.0432718682927417,0.0748546314196918,0.121552258119827 +"confidence_interval_high",0.968145973750056,0.777221904496488,0.70070494379146,0.737621923393055
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/ratio_GARP_FYMINK.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,3,4,4 +"Lower",5,4,5,5 +"Difference",0,-1,-1,-1 +"Trial_Number",10,7,9,9 +"p-value",1,1,1,1 +"probability_of_success",0.5,0.428571428571429,0.444444444444444,0.444444444444444 +"confidence_interval_low",0.187086028447399,0.0989882784425079,0.136995662265167,0.136995662265167 +"confidence_interval_high",0.812913971552601,0.815948432359917,0.787991493221132,0.787991493221132
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_hydratation.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",5,6,4,5 +"Lower",3,5,7,6 +"Difference",2,1,-3,-1 +"Trial_Number",8,11,11,11 +"p-value",0.7265625,1,0.548828125,1 +"probability_of_success",0.625,0.545454545454545,0.363636363636364,0.454545454545455 +"confidence_interval_low",0.244863216366552,0.233793597659345,0.109263443819098,0.167488094063707 +"confidence_interval_high",0.914766585862746,0.832511905936293,0.692095284988323,0.766206402340655
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_partial_specific_volume.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,3,8,5 +"Lower",5,7,8,3 +"Difference",1,-4,0,2 +"Trial_Number",11,10,16,8 +"p-value",1,0.34375,1,0.7265625 +"probability_of_success",0.545454545454545,0.3,0.5,0.625 +"confidence_interval_low",0.233793597659345,0.0667395111777345,0.246510111490575,0.244863216366552 +"confidence_interval_high",0.832511905936293,0.652452850059997,0.753489888509425,0.914766585862746
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_residue_volume.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",7,6,5,5 +"Lower",4,6,11,3 +"Difference",3,0,-6,2 +"Trial_Number",11,12,16,8 +"p-value",0.548828125,1,0.210113525390625,0.7265625 +"probability_of_success",0.636363636363636,0.5,0.3125,0.625 +"confidence_interval_low",0.307904715011677,0.210944638239297,0.110169954717117,0.244863216366552 +"confidence_interval_high",0.890736556180902,0.789055361760703,0.586620636451359,0.914766585862746
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_aa/04_outputs_aa_variables/total_residue_weight.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Ap_vs_PpPg","Pg_vs_ApPs","Pp_vs_ApPs","Ps_vs_PpPg" +"Greater",6,6,5,6 +"Lower",5,6,8,5 +"Difference",1,0,-3,1 +"Trial_Number",11,12,13,11 +"p-value",1,1,0.5810546875,1 +"probability_of_success",0.545454545454545,0.5,0.384615384615385,0.545454545454545 +"confidence_interval_low",0.233793597659345,0.210944638239297,0.138579338890161,0.233793597659345 +"confidence_interval_high",0.832511905936293,0.789055361760703,0.684222397085937,0.832511905936293
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/MutCount_concat_log.output Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,96 @@ + + ------ Occurences and frequencies of codons, amino-acids, amino-acids types ------- + +The script counts the number of codons, amino acids, and types of amino acids in sequences, +as well as the mutation bias from one item to another between 2 sequences. + +Counting are then compared to empirical p-values, obtained from bootstrapped sequences obtained from a subset of sequences. +In the output files, the pvalues indicate the position of the observed data in a distribution of empirical countings obtained from +a resample of the data. Values above 0.95 indicate a significantly higher counting, values under 0.05 a significantly lower counting. + Sequences file : concatenation.fasta + Species retained for countings : Ps,Pp,Pu,Ac,Ap,Pf,Pg,Ph,Pi + +Processing : reading input file, opening output files, building dictionaries. + Warning : countings might be biased and show high differences between species because of high variations of the indels proportions among sequences. + Frequences are more representative. + + Indels percent : + Ps : 0.174520069808 % + Pp : 1.78883071553 % + Pu : 21.8586387435 % + Ac : 9.90401396161 % + Ap : 8.98778359511 % + Pf : 15.7504363002 % + Pg : 4.31937172775 % + Ph : 5.55555555556 % + Pi : 8.11518324607 % + +Processing : resampling ... + Parameters : 200 iterations, 200 codon per resampled sequence, species used : Ps,Pp,Pu,Pf + + 10% + 20% + 30% + 40% + 50% + 60% + 70% + 80% + 90% + 100% + Done. + +Processing : countings.... + +Countings on Ps +Countings on Pp +Countings transitions between Ps and Pp +Countings on Pu +Countings transitions between Ps and Pu +Countings on Ac +Countings transitions between Ps and Ac +Countings on Ap +Countings transitions between Ps and Ap +Countings on Pf +Countings transitions between Ps and Pf +Countings on Pg +Countings transitions between Ps and Pg +Countings on Ph +Countings transitions between Ps and Ph +Countings on Pi +Countings transitions between Ps and Pi +Countings transitions between Pp and Pu +Countings transitions between Pp and Ac +Countings transitions between Pp and Ap +Countings transitions between Pp and Pf +Countings transitions between Pp and Pg +Countings transitions between Pp and Ph +Countings transitions between Pp and Pi +Countings transitions between Pu and Ac +Countings transitions between Pu and Ap +Countings transitions between Pu and Pf +Countings transitions between Pu and Pg +Countings transitions between Pu and Ph +Countings transitions between Pu and Pi +Countings transitions between Ac and Ap +Countings transitions between Ac and Pf +Countings transitions between Ac and Pg +Countings transitions between Ac and Ph +Countings transitions between Ac and Pi +Countings transitions between Ap and Pf +Countings transitions between Ap and Pg +Countings transitions between Ap and Ph +Countings transitions between Ap and Pi +Countings transitions between Pf and Pg +Countings transitions between Pf and Ph +Countings transitions between Pf and Pi +Countings transitions between Pg and Ph +Countings transitions between Pg and Pi +Countings transitions between Ph and Pi + + Done. + +Processing : creating dataframes ... +Writing dataframes to output files ... + +Done.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/aa_freqs.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,28 @@ +Species,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y +Ac_obs_counts,176.0,48.0,122.0,115.0,96.0,128.0,43.0,107.0,122.0,193.0,42.0,92.0,84.0,62.0,119.0,118.0,129.0,147.0,39.0,83.0 +Ac_obs_freqs,0.0852300242131,0.0232445520581,0.0590799031477,0.0556900726392,0.0464891041162,0.061985472155,0.0208232445521,0.0518159806295,0.0590799031477,0.0934624697337,0.0203389830508,0.0445520581114,0.0406779661017,0.0300242130751,0.0576271186441,0.0571428571429,0.0624697336562,0.071186440678,0.0188861985472,0.0401937046005 +Ac_pvalues,1.0,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Ap_obs_counts,166.0,47.0,130.0,112.0,101.0,136.0,46.0,106.0,113.0,194.0,44.0,93.0,90.0,58.0,120.0,127.0,125.0,154.0,38.0,86.0 +Ap_obs_freqs,0.0795781399808,0.0225311601151,0.0623202301055,0.0536912751678,0.0484180249281,0.065196548418,0.0220517737296,0.0508149568552,0.0541706615532,0.0930009587728,0.0210930009588,0.0445829338447,0.0431447746884,0.0278044103547,0.0575263662512,0.0608820709492,0.0599232981783,0.0738255033557,0.0182166826462,0.0412272291467 +Ap_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.870646766169,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Pf_obs_counts,143.0,42.0,117.0,112.0,94.0,127.0,46.0,102.0,99.0,189.0,41.0,84.0,88.0,46.0,103.0,129.0,123.0,123.0,40.0,83.0 +Pf_obs_freqs,0.0740548938374,0.0217503883998,0.0605903676851,0.0580010357328,0.0486794407043,0.0657690315898,0.0238218539617,0.0528223718281,0.0512687726567,0.0978767477991,0.0212325220093,0.0435007767996,0.0455722423615,0.0238218539617,0.0533402382185,0.0668047643708,0.063697566028,0.063697566028,0.0207146556189,0.0429829104091 +Pf_pvalues,0.457711442786,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.965174129353,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Pg_obs_counts,154.0,55.0,139.0,123.0,105.0,142.0,50.0,122.0,118.0,204.0,51.0,94.0,91.0,59.0,131.0,130.0,135.0,157.0,42.0,91.0 +Pg_obs_freqs,0.0702234382125,0.0250797993616,0.0633834929321,0.0560875512996,0.0478796169631,0.0647514819881,0.0227998176015,0.0556315549476,0.0538075695394,0.093023255814,0.0232558139535,0.0428636570907,0.0414956680347,0.0269037847697,0.0597355221158,0.0592795257638,0.0615595075239,0.0715914272686,0.0191518467852,0.0414956680347 +Pg_pvalues,0.457711442786,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Ph_obs_counts,173.0,53.0,123.0,122.0,110.0,137.0,50.0,119.0,107.0,190.0,51.0,102.0,92.0,61.0,123.0,140.0,127.0,150.0,44.0,90.0 +Ph_obs_freqs,0.0799445471349,0.0244916820702,0.0568391866913,0.0563770794824,0.050831792976,0.0633086876155,0.0231053604436,0.0549907578558,0.0494454713494,0.0878003696858,0.0235674676525,0.047134935305,0.0425138632163,0.0281885397412,0.0568391866913,0.0646950092421,0.0586876155268,0.0693160813309,0.0203327171904,0.0415896487985 +Ph_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,0.63184079602,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.870646766169,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Pi_obs_counts,159.0,52.0,125.0,116.0,93.0,140.0,41.0,114.0,126.0,175.0,51.0,98.0,97.0,58.0,120.0,113.0,130.0,159.0,42.0,97.0 +Pi_obs_freqs,0.0754985754986,0.0246913580247,0.0593542260209,0.0550807217474,0.0441595441595,0.0664767331434,0.0194681861349,0.0541310541311,0.0598290598291,0.0830959164292,0.0242165242165,0.0465337132004,0.0460588793922,0.0275403608737,0.0569800569801,0.0536562203229,0.0617283950617,0.0754985754986,0.019943019943,0.0460588793922 +Pi_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.303482587065,0.00497512437811,0.00497512437811,0.00497512437811,0.323383084577 +Pp_obs_counts,163.0,53.0,139.0,124.0,110.0,146.0,50.0,128.0,125.0,207.0,52.0,98.0,96.0,64.0,132.0,128.0,136.0,161.0,45.0,94.0 +Pp_obs_freqs,0.0724122612172,0.0235450910706,0.0617503331853,0.0550866281653,0.0488671701466,0.0648600621946,0.0222123500666,0.0568636161706,0.0555308751666,0.0919591292759,0.0231008440693,0.0435362061306,0.0426477121279,0.0284318080853,0.0586406041759,0.0568636161706,0.0604175921813,0.0715237672146,0.01999111506,0.0417592181253 +Pp_pvalues,0.457711442786,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Ps_obs_counts,179.0,50.0,141.0,128.0,106.0,148.0,54.0,129.0,127.0,212.0,49.0,95.0,97.0,62.0,129.0,136.0,136.0,166.0,46.0,98.0 +Ps_obs_freqs,0.0782342657343,0.0218531468531,0.0616258741259,0.0559440559441,0.0463286713287,0.0646853146853,0.0236013986014,0.0563811188811,0.055506993007,0.0926573426573,0.0214160839161,0.041520979021,0.0423951048951,0.0270979020979,0.0563811188811,0.0594405594406,0.0594405594406,0.0725524475524,0.0201048951049,0.0428321678322 +Ps_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,0.626865671642,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811 +Pu_obs_counts,139.0,46.0,107.0,116.0,91.0,107.0,39.0,98.0,105.0,178.0,39.0,87.0,75.0,52.0,97.0,105.0,94.0,114.0,37.0,65.0 +Pu_obs_freqs,0.0776102735902,0.0256839754327,0.0597431602457,0.0647682858738,0.0508096035734,0.0597431602457,0.0217755443886,0.0547180346175,0.0586264656616,0.0993858179788,0.0217755443886,0.0485762144054,0.0418760469012,0.0290340591848,0.0541596873255,0.0586264656616,0.0524846454495,0.0636515912898,0.0206588498046,0.036292573981 +Pu_pvalues,0.855721393035,1.0,0.00497512437811,1.0,1.0,0.00497512437811,0.00497512437811,1.0,1.0,1.0,0.00497512437811,1.0,0.00497512437811,0.00497512437811,0.00497512437811,0.601990049751,0.00497512437811,0.00497512437811,0.00497512437811,0.00497512437811
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/aa_transitions_freqs.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,145 @@ 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/aatypes_freqs.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,28 @@ +Species,aromatics,charged,polar,unpolar +Ac_obs_counts,218.0,521.0,533.0,793.0 +Ac_obs_freqs,0.105569007264,0.252300242131,0.258111380145,0.38401937046 +Ac_pvalues,0.00497512437811,0.950248756219,0.00497512437811,1.0 +Ap_obs_counts,225.0,521.0,540.0,800.0 +Ap_obs_freqs,0.107861936721,0.249760306807,0.25886864813,0.383509108341 +Ap_pvalues,0.00497512437811,0.706467661692,0.00497512437811,1.0 +Pf_obs_counts,217.0,477.0,512.0,725.0 +Pf_obs_freqs,0.112377006732,0.247022268255,0.265147591921,0.375453133092 +Pf_pvalues,0.00497512437811,0.706467661692,0.00497512437811,1.0 +Pg_obs_counts,238.0,561.0,564.0,830.0 +Pg_obs_freqs,0.108527131783,0.255813953488,0.257181942544,0.378476972184 +Pg_pvalues,0.00497512437811,1.0,0.00497512437811,1.0 +Ph_obs_counts,244.0,525.0,575.0,820.0 +Ph_obs_freqs,0.112754158965,0.242606284658,0.265711645102,0.378927911275 +Ph_pvalues,0.00497512437811,0.363184079602,0.00497512437811,1.0 +Pi_obs_counts,232.0,528.0,548.0,798.0 +Pi_obs_freqs,0.110161443495,0.250712250712,0.260208926876,0.378917378917 +Pi_pvalues,0.00497512437811,0.950248756219,0.00497512437811,1.0 +Pp_obs_counts,249.0,570.0,575.0,857.0 +Pp_obs_freqs,0.110617503332,0.25322079076,0.255442025766,0.380719680142 +Pp_pvalues,0.00497512437811,0.950248756219,0.00497512437811,1.0 +Ps_obs_counts,250.0,579.0,576.0,883.0 +Ps_obs_freqs,0.109265734266,0.253059440559,0.251748251748,0.385926573427 +Ps_pvalues,0.00497512437811,0.950248756219,0.00497512437811,1.0 +Pu_obs_counts,193.0,464.0,459.0,675.0 +Pu_obs_freqs,0.107761027359,0.259073143495,0.256281407035,0.376884422111 +Pu_pvalues,0.00497512437811,1.0,0.00497512437811,1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/aatypes_transitions_freqs.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,145 @@ +Species,aromatics>aromatics,aromatics>charged,aromatics>polar,aromatics>unpolar,charged>aromatics,charged>charged,charged>polar,charged>unpolar,polar>aromatics,polar>charged,polar>polar,polar>unpolar,unpolar>aromatics,unpolar>charged,unpolar>polar,unpolar>unpolar +Ac>Ap_obs_counts,191,1,1,3,4,456,3,1,0,4,468,4,4,0,8,711 +Ac>Ap_obs_freqs,0.974489795918,0.00510204081633,0.00510204081633,0.015306122449,0.00862068965517,0.98275862069,0.00646551724138,0.00215517241379,0.0,0.00840336134454,0.983193277311,0.00840336134454,0.00553250345781,0.0,0.0110650069156,0.983402489627 +Ac>Ap_pvalues,0.393034825871,0.796019900498,1.0,0.771144278607,0.766169154229,0.731343283582,0.412935323383,0.855721393035,0.00497512437811,0.437810945274,0.835820895522,0.308457711443,0.796019900498,0.00497512437811,0.293532338308,0.412935323383 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+Pu_pvalues,1.0,1.0,0.771144278607,1.0,0.00497512437811,0.905472636816,0.18407960199,0.0547263681592,0.781094527363,0.00497512437811,0.00497512437811,0.577114427861,0.721393034826,1.0,0.00497512437811,0.930348258706,0.00497512437811,0.00497512437811,0.248756218905,0.547263681592,0.00497512437811,0.621890547264,0.497512437811,0.482587064677,0.761194029851,0.796019900498,0.144278606965,0.1592039801,0.791044776119,1.0,0.985074626866,1.0,0.497512437811,0.00497512437811,1.0,0.900497512438,0.676616915423,0.870646766169,0.179104477612,0.293532338308,0.462686567164,0.442786069652,1.0,0.179104477612,0.00497512437811,0.00497512437811,0.273631840796,1.0,0.0746268656716,0.213930348259,0.601990049751,0.686567164179,1.0,0.278606965174,1.0,0.00497512437811,0.766169154229,0.402985074627,1.0,0.572139303483,0.945273631841
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/codons_transitions_freqs.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,145 @@ 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_concat/gc_and_others_freqs.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,10 @@ +Species,GC3,GC12,IVYWREL,EKQH,PAYRESDGM,purineload,CvP +Ac,0.43499127,0.41710297,0.35034904,2.25714286,1.40731707,42.61198371,-0.00581114 +Ap,0.46858639,0.42539267,0.35340314,2.16346154,1.31350114,31.12274578,-0.00910834 +Pf,0.42801047,0.3872164,0.32809773,2.29347826,1.27777778,26.61431065,-0.01812532 +Pg,0.45244328,0.43695462,0.37958115,2.21100917,1.27705628,41.44851658,-0.00136799 +Ph,0.46073298,0.43455497,0.36561955,2.06306306,1.33037694,28.21407795,-0.02310536 +Pi,0.44851658,0.42146597,0.35907504,2.44444444,1.37296037,44.5026178,-0.00949668 +Pp,0.45898778,0.44698953,0.38874346,2.18421053,1.30967742,46.39325189,-0.00222124 +Ps,0.45724258,0.45811518,0.39616056,2.19827586,1.33122363,38.39441536,0.00131119 +Pu,0.42233857,0.35536649,0.30759162,2.42857143,1.37430168,31.26817917,0.00279174
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_AT.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,-3,NaN,-2,NaN +orthogroup_544_with_4_species.fasta,33,37,32,30 +orthogroup_546_with_4_species.fasta,-1,6,3,3 +orthogroup_761_with_4_species.fasta,16,13,21,31 +orthogroup_299_with_2_species.fasta,-2,-7,NaN,NaN +orthogroup_404_with_4_species.fasta,-16,-14,-15,-16 +orthogroup_316_with_4_species.fasta,90,92,91,87 +orthogroup_487_with_4_species.fasta,-2,-4,-2,3 +orthogroup_109_with_3_species.fasta,-3,7,NaN,-5 +orthogroup_696_with_4_species.fasta,12,9,20,7 +orthogroup_442_with_4_species.fasta,20,15,17,8 +orthogroup_508_with_4_species.fasta,-18,-13,-21,-14 +orthogroup_588_with_4_species.fasta,9,20,-15,6 +orthogroup_727_with_4_species.fasta,10,9,9,12 +orthogroup_335_with_4_species.fasta,-21,-10,-5,-4 +orthogroup_660_with_4_species.fasta,4,1,1,1 +orthogroup_623_with_4_species.fasta,1,6,-3,2 +orthogroup_283_with_2_species.fasta,NaN,-2,-7,NaN +orthogroup_651_with_4_species.fasta,0,4,4,2 +orthogroup_368_with_4_species.fasta,3,13,8,11 +orthogroup_343_with_4_species.fasta,0,3,1,-6 +orthogroup_301_with_4_species.fasta,14,13,9,6 +orthogroup_707_with_4_species.fasta,-7,1,-4,-2 +orthogroup_113_with_4_species.fasta,10,21,22,29
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/DIFF_GC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,10,NaN,9,NaN +orthogroup_544_with_4_species.fasta,13,7,22,26 +orthogroup_546_with_4_species.fasta,-5,-4,-19,-11 +orthogroup_761_with_4_species.fasta,-3,-22,-8,-20 +orthogroup_299_with_2_species.fasta,-4,15,NaN,NaN +orthogroup_404_with_4_species.fasta,-2,-2,-7,0 +orthogroup_316_with_4_species.fasta,26,26,9,35 +orthogroup_487_with_4_species.fasta,3,5,7,2 +orthogroup_109_with_3_species.fasta,15,17,NaN,15 +orthogroup_696_with_4_species.fasta,-7,-8,-25,-18 +orthogroup_442_with_4_species.fasta,-8,-1,-13,-2 +orthogroup_508_with_4_species.fasta,-16,-15,-7,-10 +orthogroup_588_with_4_species.fasta,-50,-99,-102,-45 +orthogroup_727_with_4_species.fasta,-2,7,13,12 +orthogroup_335_with_4_species.fasta,4,-3,2,-13 +orthogroup_660_with_4_species.fasta,9,14,14,20 +orthogroup_623_with_4_species.fasta,10,17,16,17 +orthogroup_283_with_2_species.fasta,NaN,0,5,NaN +orthogroup_651_with_4_species.fasta,10,6,8,4 +orthogroup_368_with_4_species.fasta,16,8,-1,12 +orthogroup_343_with_4_species.fasta,-3,-8,0,-1 +orthogroup_301_with_4_species.fasta,12,9,9,16 +orthogroup_707_with_4_species.fasta,5,1,6,8 +orthogroup_113_with_4_species.fasta,16,1,8,7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/GC_percent.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,0.00679245283019,NaN,0.00672955974843,NaN +orthogroup_544_with_4_species.fasta,0.00516949152542,0.00539548022599,0.00514124293785,0.0054802259887 +orthogroup_546_with_4_species.fasta,0.00625,0.00611111111111,0.00541666666667,0.00625 +orthogroup_761_with_4_species.fasta,0.00518763796909,0.00591611479029,0.00534216335541,0.00582781456954 +orthogroup_299_with_2_species.fasta,0.00484848484848,0.00598484848485,NaN,NaN +orthogroup_404_with_4_species.fasta,0.005,0.00566666666667,0.0055,0.00533333333333 +orthogroup_316_with_4_species.fasta,0.00553571428571,0.00583333333333,0.00575892857143,0.00566964285714 +orthogroup_487_with_4_species.fasta,0.00578947368421,0.00578947368421,0.00649122807018,0.00561403508772 +orthogroup_109_with_3_species.fasta,0.00537037037037,0.00524691358025,NaN,0.00598765432099 +orthogroup_696_with_4_species.fasta,0.00502222222222,0.00515555555556,0.0052,0.0056 +orthogroup_442_with_4_species.fasta,0.00455555555556,0.0045,0.00461111111111,0.00422222222222 +orthogroup_508_with_4_species.fasta,0.00545454545455,0.00537878787879,0.00492424242424,0.00560606060606 +orthogroup_588_with_4_species.fasta,0.00548854604956,0.00569892473118,0.00565684899486,0.00541841982235 +orthogroup_727_with_4_species.fasta,0.00575757575758,0.00583333333333,0.00477272727273,0.00515151515152 +orthogroup_335_with_4_species.fasta,0.00590717299578,0.00611814345992,0.00599156118143,0.00662447257384 +orthogroup_660_with_4_species.fasta,0.00525925925926,0.00503703703704,0.00503703703704,0.00474074074074 +orthogroup_623_with_4_species.fasta,0.00598290598291,0.00606837606838,0.00615384615385,0.00589743589744 +orthogroup_283_with_2_species.fasta,NaN,0.00352941176471,0.00401960784314,NaN +orthogroup_651_with_4_species.fasta,0.00588235294118,0.0056862745098,0.00509803921569,0.00549019607843 +orthogroup_368_with_4_species.fasta,0.00533333333333,0.00551111111111,0.00493333333333,0.00542222222222 +orthogroup_343_with_4_species.fasta,0.00560975609756,0.00585365853659,0.00552845528455,0.00626016260163 +orthogroup_301_with_4_species.fasta,0.00515151515152,0.0055303030303,0.0055303030303,0.00515151515152 +orthogroup_707_with_4_species.fasta,0.00583333333333,0.00561111111111,0.00533333333333,0.00611111111111 +orthogroup_113_with_4_species.fasta,0.00505952380952,0.00532738095238,0.00541666666667,0.00556547619048
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,-0.0188679245283,NaN,-0.0125786163522,NaN +orthogroup_544_with_4_species.fasta,0.0932203389831,0.104519774011,0.090395480226,0.0847457627119 +orthogroup_546_with_4_species.fasta,-0.0138888888889,0.0833333333333,0.0416666666667,0.0416666666667 +orthogroup_761_with_4_species.fasta,0.0353200883002,0.0286975717439,0.046357615894,0.0684326710817 +orthogroup_299_with_2_species.fasta,-0.0151515151515,-0.0530303030303,NaN,NaN +orthogroup_404_with_4_species.fasta,-0.266666666667,-0.233333333333,-0.25,-0.266666666667 +orthogroup_316_with_4_species.fasta,0.133928571429,0.136904761905,0.135416666667,0.129464285714 +orthogroup_487_with_4_species.fasta,-0.0350877192982,-0.0701754385965,-0.0350877192982,0.0526315789474 +orthogroup_109_with_3_species.fasta,-0.0185185185185,0.0432098765432,NaN,-0.0308641975309 +orthogroup_696_with_4_species.fasta,0.0533333333333,0.04,0.0888888888889,0.0311111111111 +orthogroup_442_with_4_species.fasta,0.111111111111,0.0833333333333,0.0944444444444,0.0444444444444 +orthogroup_508_with_4_species.fasta,-0.136363636364,-0.0984848484848,-0.159090909091,-0.106060606061 +orthogroup_588_with_4_species.fasta,0.00420757363254,0.00935016362786,-0.0070126227209,0.00280504908836 +orthogroup_727_with_4_species.fasta,0.0757575757576,0.0681818181818,0.0681818181818,0.0909090909091 +orthogroup_335_with_4_species.fasta,-0.0886075949367,-0.042194092827,-0.0210970464135,-0.0168776371308 +orthogroup_660_with_4_species.fasta,0.0296296296296,0.00740740740741,0.00740740740741,0.00740740740741 +orthogroup_623_with_4_species.fasta,0.00854700854701,0.0512820512821,-0.025641025641,0.017094017094 +orthogroup_283_with_2_species.fasta,NaN,-0.0196078431373,-0.0686274509804,NaN +orthogroup_651_with_4_species.fasta,0.0,0.0392156862745,0.0392156862745,0.0196078431373 +orthogroup_368_with_4_species.fasta,0.0133333333333,0.0577777777778,0.0355555555556,0.0488888888889 +orthogroup_343_with_4_species.fasta,0.0,0.0243902439024,0.00813008130081,-0.0487804878049 +orthogroup_301_with_4_species.fasta,0.106060606061,0.0984848484848,0.0681818181818,0.0454545454545 +orthogroup_707_with_4_species.fasta,-0.0388888888889,0.00555555555556,-0.0222222222222,-0.0111111111111 +orthogroup_113_with_4_species.fasta,0.0297619047619,0.0625,0.0654761904762,0.0863095238095
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_AT_1000.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,-18.8679245283,NaN,-12.5786163522,NaN +orthogroup_544_with_4_species.fasta,93.2203389831,104.519774011,90.395480226,84.7457627119 +orthogroup_546_with_4_species.fasta,-13.8888888889,83.3333333333,41.6666666667,41.6666666667 +orthogroup_761_with_4_species.fasta,35.3200883002,28.6975717439,46.357615894,68.4326710817 +orthogroup_299_with_2_species.fasta,-15.1515151515,-53.0303030303,NaN,NaN +orthogroup_404_with_4_species.fasta,-266.666666667,-233.333333333,-250.0,-266.666666667 +orthogroup_316_with_4_species.fasta,133.928571429,136.904761905,135.416666667,129.464285714 +orthogroup_487_with_4_species.fasta,-35.0877192982,-70.1754385965,-35.0877192982,52.6315789474 +orthogroup_109_with_3_species.fasta,-18.5185185185,43.2098765432,NaN,-30.8641975309 +orthogroup_696_with_4_species.fasta,53.3333333333,40.0,88.8888888889,31.1111111111 +orthogroup_442_with_4_species.fasta,111.111111111,83.3333333333,94.4444444444,44.4444444444 +orthogroup_508_with_4_species.fasta,-136.363636364,-98.4848484848,-159.090909091,-106.060606061 +orthogroup_588_with_4_species.fasta,4.20757363254,9.35016362786,-7.0126227209,2.80504908836 +orthogroup_727_with_4_species.fasta,75.7575757576,68.1818181818,68.1818181818,90.9090909091 +orthogroup_335_with_4_species.fasta,-88.6075949367,-42.194092827,-21.0970464135,-16.8776371308 +orthogroup_660_with_4_species.fasta,29.6296296296,7.40740740741,7.40740740741,7.40740740741 +orthogroup_623_with_4_species.fasta,8.54700854701,51.2820512821,-25.641025641,17.094017094 +orthogroup_283_with_2_species.fasta,NaN,-19.6078431373,-68.6274509804,NaN +orthogroup_651_with_4_species.fasta,0.0,39.2156862745,39.2156862745,19.6078431373 +orthogroup_368_with_4_species.fasta,13.3333333333,57.7777777778,35.5555555556,48.8888888889 +orthogroup_343_with_4_species.fasta,0.0,24.3902439024,8.13008130081,-48.7804878049 +orthogroup_301_with_4_species.fasta,106.060606061,98.4848484848,68.1818181818,45.4545454545 +orthogroup_707_with_4_species.fasta,-38.8888888889,5.55555555556,-22.2222222222,-11.1111111111 +orthogroup_113_with_4_species.fasta,29.7619047619,62.5,65.4761904762,86.3095238095
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,0.062893081761,NaN,0.0566037735849,NaN +orthogroup_544_with_4_species.fasta,0.0367231638418,0.0197740112994,0.0621468926554,0.0734463276836 +orthogroup_546_with_4_species.fasta,-0.0694444444444,-0.0555555555556,-0.263888888889,-0.152777777778 +orthogroup_761_with_4_species.fasta,-0.00662251655629,-0.0485651214128,-0.0176600441501,-0.0441501103753 +orthogroup_299_with_2_species.fasta,-0.030303030303,0.113636363636,NaN,NaN +orthogroup_404_with_4_species.fasta,-0.0333333333333,-0.0333333333333,-0.116666666667,0.0 +orthogroup_316_with_4_species.fasta,0.0386904761905,0.0386904761905,0.0133928571429,0.0520833333333 +orthogroup_487_with_4_species.fasta,0.0526315789474,0.0877192982456,0.122807017544,0.0350877192982 +orthogroup_109_with_3_species.fasta,0.0925925925926,0.104938271605,NaN,0.0925925925926 +orthogroup_696_with_4_species.fasta,-0.0311111111111,-0.0355555555556,-0.111111111111,-0.08 +orthogroup_442_with_4_species.fasta,-0.0444444444444,-0.00555555555556,-0.0722222222222,-0.0111111111111 +orthogroup_508_with_4_species.fasta,-0.121212121212,-0.113636363636,-0.0530303030303,-0.0757575757576 +orthogroup_588_with_4_species.fasta,-0.0233754090697,-0.0462833099579,-0.0476858345021,-0.0210378681627 +orthogroup_727_with_4_species.fasta,-0.0151515151515,0.0530303030303,0.0984848484848,0.0909090909091 +orthogroup_335_with_4_species.fasta,0.0168776371308,-0.0126582278481,0.0084388185654,-0.0548523206751 +orthogroup_660_with_4_species.fasta,0.0666666666667,0.103703703704,0.103703703704,0.148148148148 +orthogroup_623_with_4_species.fasta,0.0854700854701,0.145299145299,0.136752136752,0.145299145299 +orthogroup_283_with_2_species.fasta,NaN,0.0,0.0490196078431,NaN +orthogroup_651_with_4_species.fasta,0.0980392156863,0.0588235294118,0.078431372549,0.0392156862745 +orthogroup_368_with_4_species.fasta,0.0711111111111,0.0355555555556,-0.00444444444444,0.0533333333333 +orthogroup_343_with_4_species.fasta,-0.0243902439024,-0.0650406504065,0.0,-0.00813008130081 +orthogroup_301_with_4_species.fasta,0.0909090909091,0.0681818181818,0.0681818181818,0.121212121212 +orthogroup_707_with_4_species.fasta,0.0277777777778,0.00555555555556,0.0333333333333,0.0444444444444 +orthogroup_113_with_4_species.fasta,0.047619047619,0.00297619047619,0.0238095238095,0.0208333333333
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/PLI_GC_1000.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,62.893081761,NaN,56.6037735849,NaN +orthogroup_544_with_4_species.fasta,36.7231638418,19.7740112994,62.1468926554,73.4463276836 +orthogroup_546_with_4_species.fasta,-69.4444444444,-55.5555555556,-263.888888889,-152.777777778 +orthogroup_761_with_4_species.fasta,-6.62251655629,-48.5651214128,-17.6600441501,-44.1501103753 +orthogroup_299_with_2_species.fasta,-30.303030303,113.636363636,NaN,NaN +orthogroup_404_with_4_species.fasta,-33.3333333333,-33.3333333333,-116.666666667,0.0 +orthogroup_316_with_4_species.fasta,38.6904761905,38.6904761905,13.3928571429,52.0833333333 +orthogroup_487_with_4_species.fasta,52.6315789474,87.7192982456,122.807017544,35.0877192982 +orthogroup_109_with_3_species.fasta,92.5925925926,104.938271605,NaN,92.5925925926 +orthogroup_696_with_4_species.fasta,-31.1111111111,-35.5555555556,-111.111111111,-80.0 +orthogroup_442_with_4_species.fasta,-44.4444444444,-5.55555555556,-72.2222222222,-11.1111111111 +orthogroup_508_with_4_species.fasta,-121.212121212,-113.636363636,-53.0303030303,-75.7575757576 +orthogroup_588_with_4_species.fasta,-23.3754090697,-46.2833099579,-47.6858345021,-21.0378681627 +orthogroup_727_with_4_species.fasta,-15.1515151515,53.0303030303,98.4848484848,90.9090909091 +orthogroup_335_with_4_species.fasta,16.8776371308,-12.6582278481,8.4388185654,-54.8523206751 +orthogroup_660_with_4_species.fasta,66.6666666667,103.703703704,103.703703704,148.148148148 +orthogroup_623_with_4_species.fasta,85.4700854701,145.299145299,136.752136752,145.299145299 +orthogroup_283_with_2_species.fasta,NaN,0.0,49.0196078431,NaN +orthogroup_651_with_4_species.fasta,98.0392156863,58.8235294118,78.431372549,39.2156862745 +orthogroup_368_with_4_species.fasta,71.1111111111,35.5555555556,-4.44444444444,53.3333333333 +orthogroup_343_with_4_species.fasta,-24.3902439024,-65.0406504065,0.0,-8.13008130081 +orthogroup_301_with_4_species.fasta,90.9090909091,68.1818181818,68.1818181818,121.212121212 +orthogroup_707_with_4_species.fasta,27.7777777778,5.55555555556,33.3333333333,44.4444444444 +orthogroup_113_with_4_species.fasta,47.619047619,2.97619047619,23.8095238095,20.8333333333
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nuc_variable/purine_percent.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,0.00522012578616,NaN,0.00522012578616,NaN +orthogroup_544_with_4_species.fasta,0.00564971751412,0.00562146892655,0.00576271186441,0.00579096045198 +orthogroup_546_with_4_species.fasta,0.00458333333333,0.00513888888889,0.00388888888889,0.00444444444444 +orthogroup_761_with_4_species.fasta,0.00514348785872,0.00490066225166,0.00514348785872,0.00512141280353 +orthogroup_299_with_2_species.fasta,0.00477272727273,0.00530303030303,NaN,NaN +orthogroup_404_with_4_species.fasta,0.0035,0.00366666666667,0.00316666666667,0.00366666666667 +orthogroup_316_with_4_species.fasta,0.0058630952381,0.00587797619048,0.00574404761905,0.00590773809524 +orthogroup_487_with_4_species.fasta,0.00508771929825,0.00508771929825,0.00543859649123,0.00543859649123 +orthogroup_109_with_3_species.fasta,0.00537037037037,0.00574074074074,NaN,0.00530864197531 +orthogroup_696_with_4_species.fasta,0.00511111111111,0.00502222222222,0.00488888888889,0.00475555555556 +orthogroup_442_with_4_species.fasta,0.00533333333333,0.00538888888889,0.00511111111111,0.00516666666667 +orthogroup_508_with_4_species.fasta,0.00371212121212,0.00393939393939,0.00393939393939,0.00409090909091 +orthogroup_588_with_4_species.fasta,0.00490416082281,0.00481533426835,0.00472650771388,0.00490883590463 +orthogroup_727_with_4_species.fasta,0.00530303030303,0.00560606060606,0.00583333333333,0.00590909090909 +orthogroup_335_with_4_species.fasta,0.00464135021097,0.00472573839662,0.00493670886076,0.00464135021097 +orthogroup_660_with_4_species.fasta,0.00548148148148,0.00555555555556,0.00555555555556,0.00577777777778 +orthogroup_623_with_4_species.fasta,0.00547008547009,0.00598290598291,0.00555555555556,0.00581196581197 +orthogroup_283_with_2_species.fasta,NaN,0.00490196078431,0.00490196078431,NaN +orthogroup_651_with_4_species.fasta,0.00549019607843,0.00549019607843,0.00558823529412,0.00529411764706 +orthogroup_368_with_4_species.fasta,0.00542222222222,0.00546666666667,0.00515555555556,0.00551111111111 +orthogroup_343_with_4_species.fasta,0.00487804878049,0.00479674796748,0.0050406504065,0.00471544715447 +orthogroup_301_with_4_species.fasta,0.00598484848485,0.00583333333333,0.00568181818182,0.00583333333333 +orthogroup_707_with_4_species.fasta,0.00494444444444,0.00505555555556,0.00505555555556,0.00516666666667 +orthogroup_113_with_4_species.fasta,0.0053869047619,0.00532738095238,0.00544642857143,0.00553571428571
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/A.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,24,NaN,25,NaN +orthogroup_544_with_4_species.fasta,102,100,102,95 +orthogroup_546_with_4_species.fasta,13,17,18,15 +orthogroup_761_with_4_species.fasta,117,99,116,110 +orthogroup_299_with_2_species.fasta,33,23,NaN,NaN +orthogroup_404_with_4_species.fasta,7,6,6,6 +orthogroup_316_with_4_species.fasta,195,186,188,189 +orthogroup_487_with_4_species.fasta,11,10,9,14 +orthogroup_109_with_3_species.fasta,36,42,NaN,30 +orthogroup_696_with_4_species.fasta,62,59,64,53 +orthogroup_442_with_4_species.fasta,59,57,57,56 +orthogroup_508_with_4_species.fasta,21,24,23,22 +orthogroup_588_with_4_species.fasta,487,470,457,493 +orthogroup_727_with_4_species.fasta,33,32,39,38 +orthogroup_335_with_4_species.fasta,38,41,45,38 +orthogroup_660_with_4_species.fasta,34,34,34,36 +orthogroup_623_with_4_species.fasta,24,26,21,25 +orthogroup_283_with_2_species.fasta,NaN,32,27,NaN +orthogroup_651_with_4_species.fasta,21,24,27,24 +orthogroup_368_with_4_species.fasta,54,57,61,57 +orthogroup_343_with_4_species.fasta,27,27,28,20 +orthogroup_301_with_4_species.fasta,39,36,34,35 +orthogroup_707_with_4_species.fasta,34,40,40,34 +orthogroup_113_with_4_species.fasta,88,89,88,89
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/C.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,49,NaN,49,NaN +orthogroup_544_with_4_species.fasta,85,92,80,84 +orthogroup_546_with_4_species.fasta,25,24,29,28 +orthogroup_761_with_4_species.fasta,119,145,125,142 +orthogroup_299_with_2_species.fasta,34,32,NaN,NaN +orthogroup_404_with_4_species.fasta,16,18,20,16 +orthogroup_316_with_4_species.fasta,173,183,189,173 +orthogroup_487_with_4_species.fasta,15,14,15,15 +orthogroup_109_with_3_species.fasta,36,34,NaN,41 +orthogroup_696_with_4_species.fasta,60,62,71,72 +orthogroup_442_with_4_species.fasta,45,41,48,39 +orthogroup_508_with_4_species.fasta,44,43,36,42 +orthogroup_588_with_4_species.fasta,612,659,656,602 +orthogroup_727_with_4_species.fasta,39,35,25,28 +orthogroup_335_with_4_species.fasta,68,74,70,85 +orthogroup_660_with_4_species.fasta,31,27,27,22 +orthogroup_623_with_4_species.fasta,30,27,28,26 +orthogroup_283_with_2_species.fasta,NaN,18,18,NaN +orthogroup_651_with_4_species.fasta,25,26,22,26 +orthogroup_368_with_4_species.fasta,52,58,56,55 +orthogroup_343_with_4_species.fasta,36,40,34,39 +orthogroup_301_with_4_species.fasta,28,32,32,26 +orthogroup_707_with_4_species.fasta,50,50,45,51 +orthogroup_113_with_4_species.fasta,77,89,87,90
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/G.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,59,NaN,58,NaN +orthogroup_544_with_4_species.fasta,98,99,102,110 +orthogroup_546_with_4_species.fasta,20,20,10,17 +orthogroup_761_with_4_species.fasta,116,123,117,122 +orthogroup_299_with_2_species.fasta,30,47,NaN,NaN +orthogroup_404_with_4_species.fasta,14,16,13,16 +orthogroup_316_with_4_species.fasta,199,209,198,208 +orthogroup_487_with_4_species.fasta,18,19,22,17 +orthogroup_109_with_3_species.fasta,51,51,NaN,56 +orthogroup_696_with_4_species.fasta,53,54,46,54 +orthogroup_442_with_4_species.fasta,37,40,35,37 +orthogroup_508_with_4_species.fasta,28,28,29,32 +orthogroup_588_with_4_species.fasta,562,560,554,557 +orthogroup_727_with_4_species.fasta,37,42,38,40 +orthogroup_335_with_4_species.fasta,72,71,72,72 +orthogroup_660_with_4_species.fasta,40,41,41,42 +orthogroup_623_with_4_species.fasta,40,44,44,43 +orthogroup_283_with_2_species.fasta,NaN,18,23,NaN +orthogroup_651_with_4_species.fasta,35,32,30,30 +orthogroup_368_with_4_species.fasta,68,66,55,67 +orthogroup_343_with_4_species.fasta,33,32,34,38 +orthogroup_301_with_4_species.fasta,40,41,41,42 +orthogroup_707_with_4_species.fasta,55,51,51,59 +orthogroup_113_with_4_species.fasta,93,90,95,97
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/02_tables_per_nucleotide/T.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,25 @@ +Group,Bj,Bs,Ha,Lf +orthogroup_253_with_2_species.fasta,27,NaN,27,NaN +orthogroup_544_with_4_species.fasta,69,63,70,65 +orthogroup_546_with_4_species.fasta,14,11,15,12 +orthogroup_761_with_4_species.fasta,101,86,95,79 +orthogroup_299_with_2_species.fasta,35,30,NaN,NaN +orthogroup_404_with_4_species.fasta,23,20,21,22 +orthogroup_316_with_4_species.fasta,105,94,97,102 +orthogroup_487_with_4_species.fasta,13,14,11,11 +orthogroup_109_with_3_species.fasta,39,35,NaN,35 +orthogroup_696_with_4_species.fasta,50,50,44,46 +orthogroup_442_with_4_species.fasta,39,42,40,48 +orthogroup_508_with_4_species.fasta,39,37,44,36 +orthogroup_588_with_4_species.fasta,478,450,472,487 +orthogroup_727_with_4_species.fasta,23,23,30,26 +orthogroup_335_with_4_species.fasta,59,51,50,42 +orthogroup_660_with_4_species.fasta,30,33,33,35 +orthogroup_623_with_4_species.fasta,23,20,24,23 +orthogroup_283_with_2_species.fasta,NaN,34,34,NaN +orthogroup_651_with_4_species.fasta,21,20,23,22 +orthogroup_368_with_4_species.fasta,51,44,53,46 +orthogroup_343_with_4_species.fasta,27,24,27,26 +orthogroup_301_with_4_species.fasta,25,23,25,29 +orthogroup_707_with_4_species.fasta,41,39,44,36 +orthogroup_113_with_4_species.fasta,78,68,66,60
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_AT.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,11,4,5 +"Lower",7,4,5,7 +"Difference",-2,7,-1,-2 +"Trial_Number",12,15,9,12 +"p-value",0.7744140625,0.11846923828125,1,0.7744140625 +"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667 +"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843 +"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/DIFF_GC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,3,6,10 +"Lower",7,7,7,5 +"Difference",0,-4,-1,5 +"Trial_Number",14,10,13,15 +"p-value",1,0.34375,1,0.3017578125 +"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667 +"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154 +"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/GC_percent.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",3,7,5,7 +"Lower",6,2,8,7 +"Difference",-3,5,-3,0 +"Trial_Number",9,9,13,14 +"p-value",0.5078125,0.1796875,0.5810546875,1 +"probability_of_success",0.333333333333333,0.777777777777778,0.384615384615385,0.5 +"confidence_interval_low",0.0748546314196918,0.399906426283688,0.138579338890161,0.230360541448062 +"confidence_interval_high",0.70070494379146,0.971855026522102,0.684222397085937,0.769639458551938
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,11,4,5 +"Lower",7,4,5,7 +"Difference",-2,7,-1,-2 +"Trial_Number",12,15,9,12 +"p-value",0.7744140625,0.11846923828125,1,0.7744140625 +"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667 +"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843 +"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_AT_1000.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,11,4,5 +"Lower",7,4,5,7 +"Difference",-2,7,-1,-2 +"Trial_Number",12,15,9,12 +"p-value",0.7744140625,0.11846923828125,1,0.7744140625 +"probability_of_success",0.416666666666667,0.733333333333333,0.444444444444444,0.416666666666667 +"confidence_interval_low",0.15165222980843,0.448996758963029,0.136995662265167,0.15165222980843 +"confidence_interval_high",0.723330314317894,0.922128453708956,0.787991493221132,0.723330314317894
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,3,6,10 +"Lower",7,7,7,5 +"Difference",0,-4,-1,5 +"Trial_Number",14,10,13,15 +"p-value",1,0.34375,1,0.3017578125 +"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667 +"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154 +"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/PLI_GC_1000.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,3,6,10 +"Lower",7,7,7,5 +"Difference",0,-4,-1,5 +"Trial_Number",14,10,13,15 +"p-value",1,0.34375,1,0.3017578125 +"probability_of_success",0.5,0.3,0.461538461538462,0.666666666666667 +"confidence_interval_low",0.230360541448062,0.0667395111777345,0.192232441801288,0.383803732541154 +"confidence_interval_high",0.769639458551938,0.652452850059997,0.748654517729696,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nuc_variables/purine_percent.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",4,4,7,10 +"Lower",8,5,8,5 +"Difference",-4,-1,-1,5 +"Trial_Number",12,9,15,15 +"p-value",0.3876953125,1,1,0.3017578125 +"probability_of_success",0.333333333333333,0.444444444444444,0.466666666666667,0.666666666666667 +"confidence_interval_low",0.0992460911495833,0.136995662265167,0.212666729519308,0.383803732541154 +"confidence_interval_high",0.651124493581186,0.787991493221132,0.734138652722603,0.881758896633119
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/A.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,3,7,4 +"Lower",5,3,4,5 +"Difference",0,0,3,-1 +"Trial_Number",10,6,11,9 +"p-value",1,1,0.548828125,1 +"probability_of_success",0.5,0.5,0.636363636363636,0.444444444444444 +"confidence_interval_low",0.187086028447399,0.118117248757025,0.307904715011677,0.136995662265167 +"confidence_interval_high",0.812913971552601,0.881882751242975,0.890736556180902,0.787991493221132
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/C.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",5,7,5,5 +"Lower",6,3,6,8 +"Difference",-1,4,-1,-3 +"Trial_Number",11,10,11,13 +"p-value",1,0.34375,1,0.5810546875 +"probability_of_success",0.454545454545455,0.7,0.454545454545455,0.384615384615385 +"confidence_interval_low",0.167488094063707,0.347547149940003,0.167488094063707,0.138579338890161 +"confidence_interval_high",0.766206402340655,0.933260488822266,0.766206402340655,0.684222397085937
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/G.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",4,7,5,7 +"Lower",9,5,8,4 +"Difference",-5,2,-3,3 +"Trial_Number",13,12,13,11 +"p-value",0.266845703125,0.7744140625,0.5810546875,0.548828125 +"probability_of_success",0.307692307692308,0.583333333333333,0.384615384615385,0.636363636363636 +"confidence_interval_low",0.0909203945720966,0.276669685682106,0.138579338890161,0.307904715011677 +"confidence_interval_high",0.614261661750705,0.84834777019157,0.684222397085937,0.890736556180902
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/OUT_nuc/04_outputs_nucleotides/T.csv Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,9 @@ +"","Bj_vs_HaLf","Bs_vs_HaLf","Ha_vs_BsBj","Lf_vs_BsBj" +"Greater",7,4,8,6 +"Lower",4,11,4,7 +"Difference",3,-7,4,-1 +"Trial_Number",11,15,12,13 +"p-value",0.548828125,0.11846923828125,0.3876953125,1 +"probability_of_success",0.636363636363636,0.266666666666667,0.666666666666667,0.461538461538462 +"confidence_interval_low",0.307904715011677,0.0778715462910436,0.348875506418814,0.192232441801288 +"confidence_interval_high",0.890736556180902,0.551003241036971,0.900753908850417,0.748654517729696
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/concatenation.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,18 @@ +>Ps 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phylogeny_concat.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,20 @@ +>Ac +gtacatgggcaagtttttcttcgaatgataaggtgcatatggatcattggcataatacttgggtatcttaaagtatctgttgaccattctgtccagcatccagcactggcgctgtgtgcagaagacatggtgctgcaggtgtgccactctggcacccttcttcttccacagcttctcgtgtcggccgtgcatttcagagcttcctcagcgtactccagaagagtaacaaagctctctttggagccctcgggcagaattccattggggatctccacaatgagcttccgaccaagaagcagcgtttcccagctgacctccaagcaatctgtcagagtgatacggaagcacaaactcgaggcagtctgtgccttcgccaatgtgtttacattttccggcaggccattggcgctgacagggggctcttttaacacccccacaccgttgccctctgtcttttcagacacgttgacggcgtggggctcatcaggagcaccaccgaggcccaggacccaatcgtatacaataccgcgagggcaaaccaaagccataaccgtgcattgttcctgctgctcggttttcaatgacaactccaaacaaaccacgattcacacgcgagtcttccttttctttgccacttgttgtgaacccatattcaaatacttggtttatttgattatgaggaatgccaccaccacggtcagatattcttataatgaaatcaattttgttgttggcaatagtaacagacacaggtggcatattctccagggaattcagatgattttctactgtagctctcattgcattcttcagcatctcatgtataatgtactcaagtggtggtgcaatgtatggaaaggttgcatttacatgaccattgatacgaacatctggccagatcttgttgtatacatgtccttgtcttcaggatttgacatgccatggtcttctttgggtttcactgtctctgtgcttcctggtttgtctacaagtttgactacatccttatcagatgatggagctttgttctctgactgctttgaagaacttggatcagtcttggaaatattttcacctggaagtcttgctggtctccagaactccttggcttgttccttcgtcagaatccaggcttgtttagatatatccagagcctggtctgggatgggtgacgataataagaacaatgaacatattaacctcaaggttacaggacaggatggcagtgttgtacactttaaaatcaagaagaacactcccctgaggaagctgatgaatgcatactgtgacagaacaggtgtcaagagtggagcaatgcgattccgatttgatgggcaaccaatcaatgaaacagacactccaacacagctggacatggaagatggtgatgtgattgatgtattccaacagcagactggaggcgtcgagttgacccacgtaatgcttcacgtctggacacaagggatcccagacaggctgaaccacgacgtgctgcatcgcaaccagcagcacctaccccagcacaaagattacaggctccaccatcatctggaggaagcaatgggccaatttcatctcaggatcaggaaaagactgctctcatcatgcaggtgttacaacgtgctggtgctggtgccgaactatcaggtgatgaatgtggtgatcacgtcgttcgtgttcgtctgcgccgcccacgagatccactcgctgaccgtcaagctgacggactacgccgtgccaaacgactggagaatactgctgaggaacatggtctgctttactgccgttctgatacctgtggccataacacacggtgcatttggcgtatgtctgggaattgagtattctgtggcaatgacctacagaatggtgtcatgtcaaaagcatccacttctgcatcctttaaatgaggatctttatttattgcaggatttggtggataagggtgtgagatgccacttggtaccgaggtgtccttgctcgtggcaccaactgctgtatatgaaggtggtacagtcaaaagaaatgcaacgaataaaccggagctaccagaaaaaccaaaagtttcaagaatggagcaagtttatgaaaacataccgatgtccgaacaaaaacaaggtctgcagagagacgaaagtaatggaaaacgtcaccttccattccagcttcgtggagttgatggcacaacttacgctgacctcgagatcattctggtggcttgggctggcactgatagcagatggtgctcttggtggcggtgctatgcgtgtgcctcctgggggaggtggcagtattcccgtgccatgtccacggctacgctgcttgctggcattgcttgggctaccatgctccctgtttttctttgtagctatatttatcctaatggtttggccctctttgaagccaagatccagcttaggtccagagctaagtaggtctttgttgtccttctgttcttcaagtcttcagtacaacctggtgatcatgttatcccattgtacatccctcagtgtggtgaatgcaaattctgcaaaagtccgaagaccaacctctgctcgaaaatcagagctactcaaggtgcaggtaagatgcctgatggcacaagcaggttctcttgtaatggcaaggagctgtatcacttcatgggctgcagcacattcagtgaatataccgtggttgctgaaatatctgtgtgtaaggttaatccagaagctccactgggcaaggtttgcttacttggctgtggaatatcaactggttatggagctgccttccggaactgtagctgttttcggcttcctgtcgtcgtctggtgcggaagaacgcgcgcctgtccacctggctgtgtgtgcatgttgctgtttatgcatgttcatgtcagtgcttgtgatcggtgagttagaacgagcgagtgagcgggtgcgtgagacatccgacaacatcctgtctggtcgttcactgtgtactgcttttgaatcatttcctaaaggtgaaggtcgtctcgtggctgcttgccctcgttgtgtggagtgcgtgattgaccctgtaatgttgggagccaaacataatgtactgtggcgccacctggtggagaagaatgttgagcgccaagatgatgtacatgaggtgaaaggaagccatcagcaaggcttgaggcctcatcttatgtggccggatcttgaacaactgaatccaaagaaaccgaatgccaattgcttccattccaccaatggcacagctgagcaggaacaagattccactgtgatgtgtaccttctgtccctgtatgtcaatggattttaccaggtcgccatctgtcagtgtctgtttacgttctctggaatatttgggcatgagagtatctttgagagttctatgttcagttccttgttgtctgtcatcaatggcagcaattgtccatggcaatcctaagccaaggaagacattgacagagttggacccagttacatttccaattgagttgtcagcatatttctcctgtgtggcagcctgcttgctggcaaacagatctggcaaacttgttcccagagctacaaatgtgatggcagtgacgctgtccttcaggccaaccaaacaaccgaagatagatgccaagtccccaacaacggcagtaagtagaccaatcatgataagggcaatgaagaaggctaaccagccaccccagatggaaggaggaggcacaagtgcaaaaatgatcttccagccaaaggttaagaagtgcatgatgtctgtcttcactcgactgagatccgtccccaacgctgacgtcacaaatgtccggcccccgcgctgcgggaagaccttcaccattcacttcatgcgaatcctcgaccgccgctcgttcccctccataggcctccactgcctgctgaatgaccgactggacgaaatctctgacctgcacgtggaagcccatttccaactcagacgacatatacatggacagatatctcgctacttcctggatgacgtcatcaacgttagtcttgacttccctgatccacaaggttctatgagataccttgaagccaatacaacagccctgactccacctaacagagggccgttttggtactccacagatgttgatacgaggacacaggcaccctttggtaggtcagtcctccagtgtcgcagttcacaaatatctctagttggatgtggggccatgttgttgagcacatacttcatggtggatcttgttatatatgagcgtcttgtcataatcggcagtgtagttctttactgtgccataaactgcatctatactgaggatgttgaccacttctatacgatcaaagtaaataatgacacctccactggtaccacatggtacattcttgacctcatctgtttgacaatgtcactgccagaccagccacataacacagggctctccagggctgcagggacagctgatagcacaacgtgtgcagtatccgcgaaaaggcgaagatccggaaatgccaaagggccacctcagtcgacggcgacgtcagtacgtaaaggaaaccaatcagcacgaaagggggaatgttctccatgtcatgtcatcagatcggcaatgttcttttccaggtcatcaattctgtgtcccatgtcatctattcttgtgataacttggtcggacatgttctggaatttatcctgcatctgctgtaaaaggttttgcacatattgtgttagatcctgtatgtctttaggatcggcactgttggtgataaaaaagaagcctaatatttttccacccaaatgttttcgtcttgcctcttcatggtccataatcccacctgatgttgtgagcacaatgtacccaaactgtcttgatggcagtaggttagttgtccatttctccatgtctctgatgcaaacatcaaaccttggacttatcacaccacacttgttcagtcttcctgtcaaattaacaacaatttttcctgctctgtggtcatcaatgatctcaaactcaccaatgaaaagtgtgcggtatatgttccttcctaattttgtcctaaactggatgtatgcctctggatcatccttttctggatcttttgttgtatctgtgagaactgcttccatttcagcctctttttcttcctccttgctcataatttctgctctaaccttatcaagcaaggcatactgtgacatctgctgtatgatgacaggagctggtggtggactgtgcagactggccatgccagccagactcgtcatgcttgctgaaccattcatcatttgctgctgttgctgctgtgttagctgctgtggtttaactttgcacacattgctatggtccagttcattcttgttactggtgtttagatctgatgaggacatcacagacgtggcactctgtgcagaggtaatattttctgtgaggttcttcatgagttcggtaagtttgctagtcagatcttcatctggctgctttgccgacgttgttggtatcgttggtcgttcatgtgatgtagtcggcagatgttctgatttcgtgttctgcgctgtcgttggacttggtaaggactgggtcggtggcgccgcggtgccgtcgcggccaagactgcagtcatcagagtccgatgttagtgtgaacgtggctgggcaggaaacacgcagaccaattgacctcagtgagccatccagcggagaactgacacctggacaaggatccgaggctcggggatctacaacacgaggggctgaagctaagggatccacacccagagattctgaggtcataacatggatggggtcgacattgccaagcttcttggtgtgtgttttcagtggcagtggtggtggtggtgttgatttcactggtgactgtgcaggactcgagtctcctattgatgtgtcctcctcaataatgccctcatccgtgtgttcagcatctgcaggaagtggattggcagttatgcgtatgctgcactcggatcctttaaaccacagtgattcccattccagggaggcagatgccgtttccatggattcagacacatttagtgttgatggtagcagacgtttgaagtcaatcgtttgcttgcctcatgacagacaacagaacatctctgatgatgaattgaactccaaacatacgaagaaatcacataaattgaagaaagtgaaaagacatcaaaagagaaaaaagaaatcttccattttgggcgaatcaggatcttgcacaagtggtgattcagtggactctggagaggcggtcgcttccggcatctcttcagtgttgtcaggatctgtgatgtcttgtacaagaggttcattagatatatcctctattattgtatccgagggatccgtaacatgggcgaagtgccatctaatgccatcgttactgcctcttttaaatcggaacaagaaagagaaatctactggacgctcatcaactatgctcagcagttctttgcctctgataacaatgaagattttgccatgttttcttcaccaatgcttgaatacaaagactcagcctctttgtcatcagctggtttgtcttccacagtttcagtttccattggttcctcctcatcctctttggatgcctcctcagcagcagcctctgtacgtatcttttcctctgcctccttggcagcccttcttccacttcttcttctgggactttcatcttcctcctgttccttggcactggaccttccctttctggttgctttgcgaggcgatggtgttttcaactttttcacttcctcttcctctggctggtactcctcttcctcttcctcctcttcaccctgtgattttcgtccttgacctctcctgccacgtgaactccggccagcacctcgaccagtgcctctgccacgtggctttgactgtgagcacccatcttatcatttgcatgacatacggcacaactcttttcgtaatcctcctgacctggagctaccgtatccttcttcttagggaggtctcgaacttcgctaaatggtggattgacatcggttcgtgggtctttcaccacaaccaacttagccccatcatcttcacaatctttcatacatcgcttcccaattgctccaatattcttgccatccagtgtatgtgtgtgaaagcatgtgtagaactggtactgccagccaaatcacagcatcgtttagaagatgcccacgccgtctacgtggtgggagtccacacacacacacacgtactaaggactaagttcatagagatgctatactcaacaagaaaaagtcactatcatacagtgattacccatcacttagtgcagacaaacacatcaccattacattttccatcaacaacagtccatggatttacagattttgtcttagttgcgactttcctactgtttttagtaattctgcccgactgcatgctgcccactggttttaggtttaccttggctgttgatttgtacgattgcttacgtggcgctggaagtgttttggcgtcactggctggcaggttgttttcatctcttgttgtaagcggagcacgcaatttcttgctggagttatgcctcggtaccggcacgtcagccagcctatcagggacggatgttttgctgacgtcaccaaggcttgccgatgagcggcgttttgattcgctgctgcgtcgattccttccggaactgccgacagacgaatcggccaatgacgtcaacgaactgggacggctgctcgtacttccggcgcgcgactgcggcctctggttgctgaataatgaactacttccattcatgtgggcatcaagcttaggccctttctgtgacagtctctccagcgtgtcgtcgctgacagtctcgtttgcctctttttctaactccaaccgaaatatatatctcgtgctgcccttcttaatatcagtaacgtttacgctgtattggccttccagtgagctgtccttgagtacatcctctgttagtttagtaaatgttgccgcttcctttatgtacttacacactctagctatatcttcacatgatgcaccatattccattgctaaggcagcctcattaataagttctccagcaaccgaagcaacaatatgtacaccaagaactctgtccgactctttatctccaataacttttaccaagccatctgtatcattgttagtttttgcccgactgtttgctgccaaaggaaactttcca--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Pu +cctgcggcaacatcgcctgttcacgtcgaacccgaagctggactgctgcccgacgataaccgagctgacccagcgggcggcgggcatcaacccgcagggcctgctcctcgagctcttccacacgcccaacttcacacagacgttctacgagacggcctgccacccggcgatcaagggccggccgtgccagttcatcgaccgccagtacgcggcgtacagcaagtgcatacagcagtactcgtacgtgtacgcgctcgggcggacgtacgg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +>Am +aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +>Ap +tctgatccatccataatggctgcatccatctggacttctcctttggcatttagggctgatccagtacctgcatcaaacacagagttgttctccatatccatgacagccaattccacaacatctagagcagatccaccatttaataagagctttaaccctttaagtgcagcctttttaaccccttgtctgttttgcatggccatgctgtctgggatggcccaagctccacca--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Pf +tgtagcattaccatgtattggcattccactctccgtcatgttgacaaccaccgttccggcgagtccaaaatcatcttcaaagatataatctggtattgttatgttaatgtcatagagagtcggaaagtgattttcagttttatactgatgcgtgtatattttgccgtatccatgcacctctattgtccaccatccgtgtttacaaggatgatgttgttgtatcgttccctcgagataaccatttctaacttgttgttcgcgccatctcttcacgtactggccggcgccatctcgaaggtatatgtccacagcgccatgtgg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +>Pg +gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Ph +cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +>Ps +acatggagtagcattggtcgaccacgagtcaatggcaagcttgagatgacaaggagtatcggtgatgttgcggtgtcggcatgcggtggctccctcatggtggcaacaaggagaactacagctctgctcgaaactgatgatatattcaaacacaaagatgtgatatgtttaggtgtaatattttgtatgatattcttggtgaccttgcttcttgtggcagcgaccttcacctcacgaccattgagcgcagactttctgtcatcttcaaggaagacaaaatgtgtcatggcatggatactcgcgtatcccattgtaatcatctttttcgtttatatacgttactaccaagacgaggattgcatagatctgacaccttatattatacctcaggttgacaagacttattgtggtgctaatcttgatgacttctataaaaagtccatgttgacatttgaagcttatgtcattgccctggttggtgctgtactagtagtcttaagtatgttccatctgatgcacactgcagccaattacattcagatccacgaatctgggccgacgaattacgatatttataagaacgaagtggccaataaacatccatcgggatca------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +>Pp +acacagaaggaagcacagagggcctaccaagaagaactaaagagacagattgaggagcagaagctgataaaacaaagggaaaaggaagagagagaaagatacgataagaagctagatgacgaaattaggaactatgacccctttggacgaggtggtggaggagcaccaatggatggtgaatcgtttgctagaggtggtcatggtatctttggtgaaccattgtctgatgct--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Pa +gagctgtcctttgtgctgtcatctttaacatttatagccacatttctgtttgcatcacttgccatgaagaattaccatggcaacaagtatccaccaatttggtttcctagtgatggtggcttcacctatcatgtgataagtacagcgtctgagtggataatgggatgtagaaaatggtacgactatgcctgtaagccaatggattattacacagaaacaaaaatcttgcaagaaaagattgtcctagaagccaatagtgatgacttttttacagtagctatccgtccacatggaatctttggcccacgtgacccgcacatggtgcccactactgtacgcactgccaaggcaggaaaaatgaagttcaaaataggcgatgggaaaaatattgtggatttcacttttgtggaaaatgttgttcatggtcacatt------------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_3sp_2.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,6 @@ +>Pg1Pg2_ContigI_295 +YGLYKQATVGEINTDRPGMLDFKGKAKWDAWE +>Pp_2630_2/3_0.667_949 +YGLYKQVTVGDVNAARPGMLDFKGKAKWDAWE +>Ap3661_1/2_1.000_1488 +YGLYKQATVGDVNTDRPGMLDFKGKAKWDAWE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_3sp_7.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,6 @@ +>Ac10784_3/3_0.600_925 +DLRSNLSNYKLQLQQVEAALALDQENEDLKKLQKD +>Pf1355_1/1_1.000_940 +DLRTNLSNYKLQLQQVEAALALDQENEDLKKLQKD +>Ap11551_1/2_1.000_2287 +DLRSNLSNYKLQLQQVEAALALDQDNEDLKKLQKD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_4sp_4.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Pg1Pg2_ContigI_830 +RHVECFTCSMRKFILFGTILPPTRLLTITPTACVTLYTRSLAMIIFVWHTFLDCSITLYIHNVTNFINFHIS +>Pf879_1/1_1.000_626 +RHLECLTCSIRKFILLGMILPPTRLFTITPTACVTLYTRCLAMVIFVRHTFLDCSITLYIYDITNFIHFHVS +>Ac197_2/2_1.000_643 +RHFECLTCSIRKLILLAMILPPTRLLTITPTACVTLYTRSLAMVVFVRHTFLDSSISLNIHYVTHFVHFHIG +>Pp_589_1/1_1.000_552 +LHFECFMCSIRRLILFGMILPPTRLLTITPTACVTLYIRCLAMVIFMRHSFLDCTMTLDIHNIPYFVHFHIR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_4sp_6.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Pg1Pg2_ContigI_1514 +PGLCLECYTCVRQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWKPHGDRIHFINKGCMRYERCLDWQVSKRHTCRRDWYLDWECVECCRGDMC +>Ap3180_1/2_1.000_1116 +PGLCLECYTCVNQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWRPHGDRIHFINKGCMRFEKCLDWQVARRHTCRRDWYLDWECIECCRGDMC +>Ac2018_1/1_1.000_627 +PGLCLECYTCVNQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWRPHGDRIHFINKGCMRFERCLDWQKSRRNTCRRDWYLDWECVECCRGDMC +>Pf2190_1/1_1.000_917 +PGLCLECYTCVRQDNNKDKCIKTTIQCEEYENGCYSQIRWGIPPYWKPHGDRIYFINKGCMRFEKCLEWQKLKRHTCRRDWYLDWECVECCRGDMC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_10.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Ap5723_1/1_1.000_1183 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA +>Ac8933_1/2_1.000_1159 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA +>PsIsotig20888_13433_1513 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPLA +>Pp_2523_1/1_1.000_2145 +CFNGYEHTSDYVGKAYFGCWWIFHKEYSYVRDWIMPSWFIACQTLMTFAIVTMFITLGLFPMA +>Pg1Pg2_ContigI_6331 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPMA +>Pf1268_1/1_1.000_688 +CFNGYEHTSDYVGKAYYGCWWIFHKEYSYIRDWIMPSWFIACQTLMTFAIVTMFATMGLFPLA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_11.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>PsContig23463_00014_509 +GDDAAQKQEILDWIEAVTGSKIPRDQPFEKILKDGVILCNLMNKIMPGSVKRINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGFDGPTIGPKMAEKQEREWTEDQLREGRQGIIGLQAG +>Pf344_1/1_1.000_2337 +GDDAAQKQEILDWIEAVIGSKIPRDQPFEKILKDGVILCNLMNKIMPGSVKRINKKGGNFALMENIAAFQKAMKDYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGFDGPTIGPKMAEKHEREWTEDQLREGRQGIIGLQAG +>Pg1Pg2_ContigI_5539 +VDDAAQKQELLDWIEAVSGSKIPRDQRFEKILKDGVILCNMMNKIVPGSVKRINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLNKGYDGPTIGPKMAEKHEREWTEDELREGRQGIIGLQAG +>Pp_115_7/8_0.421_2349 +GDDAAQKTEILDWIEAVTGTKIPRDQPFEKILKDGVILCNLMNKITPGSVKRINKKGGNFALMENIAAFQKAMKSYGVPEEEVFQTADLFEARNVKAVVKSLNALGRTCLNKGFDGPSFGPKMAEKHERQWTEDELREGRQGIIGLQAG +>Ac261_5/5_0.871_1061 +GDDAAQKQEILDWIEAVTGDKIPRDQPFEKVLKDGVILCNLMNKIMPGSVKKINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLAKGFDGPTIGPKMAEKQEREWTEDQLREGRQGIIGLQAG +>Ap77_5/8_0.405_866 +GDDAAQKQEILDWIEAVTGDKIPRDQPFEKVLKDGVILCNLINKIMPGSVKKINKKGGNFALMENIAAFQKAMKAYGVPEEEVFQTVDLFEARNVKAVVKSLMALGRTCLAKGFDGPTIGPKMAEKHEREWTEDQLREGRQGIIGLQAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_16.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Ap3513_1/1_1.000_737 +KIGTVGISHYAQEALGDIVFAELPEVGSEFVKDDECGTLESV +>Pp_7121_2/3_0.778_2103 +KIGTIGISHYAQEALGDIVFAELPEDGAEFDKDDECGTLESV +>Pg1Pg2_ContigI_3765 +KIGTIGISHYAQEALGDIVYAELPEVGSEFNKFDECGTLESV +>Pf199_1/1_1.000_306 +KIGTVGISQYAQEALGDIVYAELPDVGSEFNKHDECGTLESV +>Ac4439_1/1_1.000_890 +KIGTVGISHYAQEALGDIVFAELPEAGSEFVKDDECGTLESV +>PsIsotig06983_01306_1511 +KIGTVGISQYAQEALGDIVYAELPDVGSEFTKHDECGTLESV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_18.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Ac3728_1/2_1.000_2558 +AMLHLMLPGTVITYYGEEIGM +>Pp_1484_1/1_1.000_2519 +AMVHLMLPGTAITYYGEEIGM +>Ap459_1/1_1.000_2245 +AMLHLMLPGTAITYYGEEIGM +>Pf737_1/1_1.000_940 +AMLHLLLPGTAITYYGEEIGM +>Pg1Pg2_ContigI_2873 +AMLHLMLPGTAITYYGEEIGM +>PsContig14622_00221_1814 +AMLHLMLPGTAITYYGEEIGM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_25.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pg1Pg2_ContigI_440 +DGGGNLLVAADSYIGEKIRDLAVECGIEFDEEGTSVIDHHNYDVNDDGKHTLIVADPDNLVTAPLLTGSETHNPLLFKGVGMTADPDNPLVISILHASSSSYSFDPNSPITDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKASGGKKYAKSGNQQLALRLSQWVFKEKGVLRVGKVTHHKKGEKEPPVAYTIMDTVEYTIEIEQFEDGKWMPLVADDVQLEFVRIDPFVRMGLRKKGGKFYAKFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLEHTQYE +>Pf3990_1/1_1.000_914 +DGGGNLLVAADSYIGETIRDLAVECGVEFDEEGTAVIDHHNYDVKDDGKHTLIVADPENLVNAPVLTGTEKHNPLLFKGVGMTADPDNPLVISILHASSSAYSFDPDSRINDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKAGGGQKYAKSANQELATRLSQWVFKEKGVLRVGKVTHHRKGEKEPPVAYTIMDTVEYTIEIEKKEGDKWLPLDANDVQLEFVRIDPFIRMGLRKKGGKFHAEFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLQHTQYE +>Pp_205_1/1_1.000_1576 +DGGGNVLVAADSYIGETIRDLAGECGVEFDEEGTSVIDHLNYDVKDNGKHTLIVANPDNLVNAPMLIGSEKHNPLLFKGVGMTADPDNPLVINILHAASSAYSFDPDSRIQDYPHAVGKNTLLIAGLQARNNARVLFFGSLDFFSDETFNAPVQKSGTTQKYSKSGNQHLALRLSQWVFKEKGVLRVGKVVHHKEGEKEPPMAYTVMDIVEYSVEIEKNEDGKWMPLDAKDVQLEFVRIDPFVRMALTKKGNKFYAKFKIPDVYGVYQFRVDYNRIGYTHLFITTQVSVRPLQHTQYE +>Ap3808_1/1_1.000_2053 +DGGGNVLVAVDSYIGETIRNLAGECGVEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLINAPLLTGNEKHNPLLFRGVGMTADPDNPLVINILHAASSAYSFDPDSRITDYPHAIGKNTLLISGLQARNNARVLFVGSLDFFSDETFNAPVQKANGGQKFSKSGNQQLATRLSQWVFKEKGVLRVGKVVHHKVGEKEPPAAYTIMDNVEYSVEIEKNEDGKWVPLDADDLQLEFVRIDPFIRMPLSKRGNQFYAKFKIPDVYGVYQFRVDYNRVGYTHLFITTQVSVRPLEHTQYE +>Ac3918_1/1_1.000_1754 +DGGGNVLVAVDSYIGETIRNLAGECGVEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLINAPLLTGSEKHAPLLFRGVGMTADPDNPLVINILHAASSAYSFDPDSRITDYPHAVGKNTLLISGLQARNNARVLFVGSLDFFSDETFNAPVQKANGGQKFPKSGNQQLATRLSQWVFKEKGVLRVGKVVHHKVGEKEPPAAYTIMDNVEYSVEIEKNEDGKWLPLDADDLQLEFVRIDPFIRMPLTKKGNQFYAKFKIPDVYGVYQFRIDYNRIGYTHLFITTQVSVRPLEHTQYE +>PsIsotig14896_07441_3814 +DGGGNLLVAADSFIGETIRDLAVECGIEFDEEGTSVIDHHNYDVKDDGKHTLIVADPENLVSAPMLTGTEKHNPLLFKGVGMTADPDNPLVISILHASSSAYSFDPNSRITDYPHAVGKNTLLISGLQARNNARVLFFGSLDFFSDETFNAPVQKAGGGLRYAKSGNQLLALRLSQWVFKEKGVLRVGKVTHHKKGEKVPPVAYTIMDTVEYTIEIEKNEDGKWVPLDADDVQLEFVRIDPFVRMGLHKKGDKFYAEFKIPDVYGVYQFRVDYNRIGYTHLFVTTQVSVRPLEHTQYE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_27.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pf1236_1/1_1.000_402 +LLWSEILRLVPFTSVELAQVRLLRLVHHCHDPC +>PsIsotig05584_00818_503 +LLRSQILWLVLFTSVKLPQIGFLCLVHHRHDPC +>Pp_3399_1/1_1.000_348 +LLWSQILRLVFLIFVELAQILLLRLVHHCQYTG +>Ac363_1/1_1.000_432 +LLSPQVLWLVLFTFVKLAQVFLLCLVHHRHDSG +>Pg1Pg2_ContigI_2596 +LLRSQVLWLVLFTTIKLSQVVLLCLMHHRHDSC +>Ap1830_1/1_1.000_511 +LLSPQVLWLVLFTFVKLAQVFLLCLVHHCHDSG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_30.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pf1581_1/1_1.000_1837 +NWAVFENDMKWKPMEKRK +>Pp_1355_1/1_1.000_1833 +NWAVFENDMKWKPMEKRE +>Ac1659_1/1_1.000_1848 +NWAVFENDMKWKPMEKRK +>Pg1Pg2_ContigI_3242 +NWAVFENDMKWKPMEKRK +>PsIsotig07835_01762_1971 +NWAVFENDMKWRPMEKRK +>Ap3485_1/1_1.000_1864 +NWAVFENDMKWKPMEKRK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_32.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>PsIsotig12291_04836_2510 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFEAELYQSEYTIEDEQLKALLATSASRKAAKKKKK +>Pf61_1/1_1.000_1008 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFEADLYQSEHTIEDEQLKALLATSASRKAAKKKKK +>Ac1652_1/1_1.000_2305 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMRITGLPLDLDIYQSEYKIEDEQIKSILATSASRKAAKKKKK +>Ap914_1/1_1.000_2326 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMRITGLPLDLDLYKSEYKIEDEQIKSILATSASRKAAKKKKK +>Pg1Pg2_ContigI_2687 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMKITGLPFETEIYESEHTIDDEELKTLLATSASRKAAKKKKK +>Pp_3975_1/1_1.000_1535 +LDARTTVYKKKDMLYNLKMKASRQFFSEVEKKFGTMPFTLRMFEDERKAKMGVVECVKHDLVEGFNVLWEREGEYVAQFKFTLLLMPNGPMMITGLPFDPDLYQSEYSVEDEKLKGLLAMSASRKAAKKKKK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_35.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>PsIsotig06251_01036_1545 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVTCGFSGFCLHGFWCLVFIVMGWHLC +>Ac7666_1/1_1.000_1396 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSTKFTRDLFKVACGPCCFCLHGIWSVVLVTLGWNLC +>Pg1Pg2_ContigI_275 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVTCGSSGICIYGIRCLVPIVVGWHLC +>Ap4162_1/1_1.000_589 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSTKFTRDLFKVACGPCCFCLHGIWSVVLITLGWNLC +>Pp_3408_2/2_1.000_676 +NRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTSSKFTRDLFKVTRGTSSFCIHGIWCIISLAVGWNLC +>Pf3031_1/1_1.000_540 +SRYVSPINPAVFPHLTVVLLGIGIFFMAWFFVYEVTASKFTRDLFKVARSFSGFCLHGLWCIVLVVMGWYLR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_38.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pf4498_1/1_1.000_1098 +FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSASPQHSPPAKYSKKEARDNNKYYSKEYENHYDRDYHHRDSRHEHERSKHKRRRHTPTYSPVRSYSRSPEPRSKAHKKYYKEKYRA +>Pg1Pg2_Pg13774_1/1_1.000_1948 +FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSASPQHSPPAKYSKKEARDNNKYYSKDYENHYDRDYHHRDSRHDHERSKHKRRRHTPTYSPVRSYSRSPEPRSKTHKKYYKEKYRA +>Pp_3267_1/2_1.000_1460 +FVGGTRKKRSRSRTRSNSKSRSYSSQESNSTGSPQRSPPVKFSKKEARDNNKYYSKEYDNHYDRDYHHRDSHRDHERSKHKRRRHTPTYSPIRSYSRSPEPRSKTHKKYYKEKYRA +>Ac4272_1/2_1.000_2412 +FGGGSRKKRSRSHTRSNSKPRSYSSQESNSTASPQHSPPAKYSKKEARDNNKYYSKEYDNHYERDYHHRDSHHDHERSKHKRRRHTPTYSPLRSYSRSPEPRSKTHKKYYKEKYRA +>Ap3418_1/1_1.000_1919 +FGGGSRKKRSRSHTRSNSKTRSYSSQESNSTASPQHSPPAKYSKKEARDNNKYYSKEYDNHYERDYHHRDSHHDHERSKHKRRRHTPTYSPLRSYSRSPEPRSKTHKKYYKEKYRA +>PsIsotig12297_04842_646 +FGGGSRKKRSRSHTRSNSKSRSYSSQESNSSVSPHRSPPVKYSKKEARDNNKYYSKEYENHYDRDYHHRDSRHDHERSKHKRRRHTPTYSPVRSYSRSPEPRSKAHKKYYKEKYRA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_39.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>PsIsotig10643_03194_2284 +ITHVLNITAHVPFHFEAEGIVYKRLPATDSGHQNLKQYFEDAFKFIEERFRR +>Pp_6073_1/1_1.000_1725 +ITHVLNVTGHVPLHFEAQGIIYKRLPATDSGQQNLKQYFEDAFKFIEEKLWR +>Pf4635_1/1_1.000_231 +ITHVLNITAHVPFHFEAEGIVYKRLPATDSGHQNLKQYFEDAFRFIEERFKR +>Ac2807_1/1_1.000_2307 +ITHVLNVTAHVPFHFEEQGIIYKRLPATDSGHQNLKQYFEDAFTYIEEKFKW +>Pg1Pg2_ContigI_3109 +ITHVLNVTSHMPFHFEAQGITYKRLPATDSGHQNLKQYFEDAFKFIEETFRR +>Ap5088_1/1_1.000_2170 +ITHVLNVTAHVPFHFEEQGIKYKRLPATDSGHQNLKQYFQDAFTFIEETFRW
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_40.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Ac1381_1/2_1.000_1229 +MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTSQMEKNLMRKLKKKGIPGKFIARGGGKPGEAIISAADDEDADMIVMATRGRGRLMRVLLGSVS +>Pp_1351_1/1_1.000_1516 +MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTAQMEKALMRKLKIKGTPGKFITRGGGKPGEAILSAADDEDVDMIIMATRGRGKLMRVLLGSVS +>Ap2493_1/2_1.000_1233 +MHSFELPLMHSYEEMYVSPDMWQATLKKEAERTSQMEKNVMRRLKKKGIPGKFIARGGGKPGEAIVSAADDEDVDMIVMATRGRGRLMRVLLGSVS +>PsIsotig15400_07945_928 +MHCFELPLMHSYEEMYVSPEMWQATLKKEADRTSHMEKALMKKLKIKGIPGKFIARGGGKPGEAILSAAEDENVDMVVMGTRGRGKLMRVLLGSVS +>Pf1400_1/1_1.000_761 +MHCFELPLMHSYEEMYVSPEMWQATLKKEADKTAQMEKTLMRKLKIKGISGKFIARGGGKPGEAILSAAEDEDVDMIVMGTRGRGKLMRVLLGSVS +>Pg1Pg2_ContigI_142 +MHSFELPLMHSYEEMYVSPDMWQATLKKEADRTTHMEKVLMKKLKLKGVPGKFIARGGGKPGEAILSAAEDENVDMIVMGTRGRGKLMRVLLGSVS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_41.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pf645_1/1_1.000_1413 +NSDLDTMTALGSRIRWITRRLGFLSRRVSTTSIVARTVFVALKSAFLQNSPSICSQGLAFSRTICMHVE +>Pg1Pg2_ContigI_3539 +NSDLDTITALGSRIRWITRRLGFLSRSVSTTSIVARTVFVALKSAFLQNSPSICSQGFAFSRTICMHVE +>Ap5964_2/2_1.000_2574 +NSDLDTMTALGSRIKWMTRRLGFLSSSVSTTSIVARTVFVALKSAFLQNSPSICSHGLAFSRTICIQVE +>Pp_3400_2/2_1.000_2104 +NSDLDTMTALGSRIRWITLRLGFLSSSVSTTAMVARTVFVALKSAFLQNSPSICSQGFAFSLTICIQVE +>Ac3315_3/4_0.828_2597 +NSDLDTMTALGSRIRWITRRFGFLSSSVSTTSIVARTVFVALKSALLQNSPNICSHGLAFSRTICMQVE +>PsIsotig06401_01089_2384 +NSDLDTITALGSRIRWITLRLGFLSSSVSTTSIVARTVFVALKSAFLQNSPNICSQGFAFSLTICMHVE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_46.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pp_882_1/1_1.000_2312 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLALLIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRRQLLIYENINKEMDKTLSEIKKLLEKQKVADEQEKLRRIQEERERERKKKEEEERKQREEEEQKKLKAEMET +>PsIsotig15436_07981_1677 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLAALIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRRQLLIYESINKEMDKTLAEIKKLLEKQKVAEEQERLRRIQEERERERKKKEEEERRKREEEEQKRLKAEMEA +>Pf127_1/1_1.000_1072 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLAALIKKVKIWLIKSRWRKAQWGVLSVIKLKNKIIYRRQLLIYEGINKEVDKTLVEIKKLLEKQKVAEEEERLRRIQEERERERKKKEEEERRKREEEEQKKLKAEMEA +>Ap1670_3/5_0.667_5194 +FKFGLTKVFFRPGKFAEFDKIMTSDPENLATLIKKVKVWLIKSRWRKAQWGTLSVIKLKNKIIYRKQLLIYEGINKEMDKTLAEIKKLLDKQKVAEEQERMRRIQEERERERKRKEEEERKKREEEERLRLKAEMEA +>Ac2574_1/1_1.000_4696 +FKFGLTKVFFRPGKFAEFDKIMTSDPENLATLIKKVKIWLIKSRWRKAQWGTLSVIKLKNKIFYRRQLLIYEGINKEMDKTLAEIKKLLDKQKVAEEQERMRRIQEERELERKRKEEEERKKQEEEERLRLKAEMEA +>Pg1Pg2_ContigI_2586 +FKFGLTKVFFRPGKFAEFDQIMKSDPENLALLIKKVKLWLIKSRWRKAQWGALSVIKLKNKIIYRRQLLIYESVNKEMDKTLTDIRKLLEKQKVAEEQERMRRIQEERERERKRKEEEERQKREEEEQKRLKVEMEA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_47.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pg1Pg2_ContigII_47 +QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>Ac120_1/1_1.000_522 +QKDIKDGKYSQVLSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>Ap1431_4/4_0.500_851 +QKDIKDGKYSQVLSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHMKTTGRRGRTVGVSKKK +>Pp_11407_1/1_1.000_522 +QKDVKDGKYGQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>Pf74_1/1_1.000_506 +QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK +>PsContig17553_00005_681 +QKDVKDGKYSQILSNVLDSKIREDLERLKKIRAHRGLRHYWGLRVRGQHTKTTGRRGRTVGVSKKK
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_50.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Ac2592_1/1_1.000_1693 +ERAMAPAGDGAFTIGKGVLAGASAVGLGMLCYYGLGMSNQVGAIDRAAIWPEEVRQRIKDTYMYFGGSLIFTAASAVAVSRSPVMMRLVMRNGWLTIIGTMAAMIGSGMVVRSLPYKKGFGAKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYALQPYDPINNSVGIYLDTINIFIRIATILAGG +>Pf687_1/1_1.000_1628 +ERAMAPAGDGAFTVGKGMLAGVSAVGLGMLCYYGLGMSNQVGAIDRAAIWPNIVRQRIKDTYMYFGGSLIFTAASAVAASRSPFMMRLVMRNGWLTIIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYAVQPYDPINNSVGIYLDTINIFIRIATILAGG +>PsContig29267_00170_1133 +ERAMAPAGDGAFTAGKGMLAGVSALGLGMLCYYGLGMSNQVGAIDRAAIWPNIVRQRVKDTYMYFGGSLIFTAASAVAASRSPVMMRLVMRNGWMTLIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMIHSGIVGAVIAPITLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYAVQPYDPINNSVGIYLDTINIFIRIATILAGG +>Pp_2968_1/1_1.000_1595 +ERAMAPAGDGAFSIGKGLVAGMSAVGLGMLCYYGLGMSNQVGAIDRAAIWPDIVRQRVKDTYMYFGGSLMFTAASAVAASRSPMVMNLVMRNGWLALIGTMAAMIGSGMIVRSLPYKEGFGAKQIAWMVHSGVVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAVCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGLYSVAMYGGLALFGAFLLYDTQKIIHRAENHPVYANQPYDPVNNSVGIYLDTINIFIRIAMIMGGG +>Ap2039_1/1_1.000_1819 +ERAMAPAGDGAFTIGKGVLAGASAVGLGMLCYYGLGMSNQVGAIDRAAIWPDVVRQRIRDTYMYFGGSLIFTAASAVAVSRSPVMMRLVMRNGWLTIIGTMAAMIGSGMVVRSLPYKEGFGSKQIAWMVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSLGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIYRAENHPVYALQPYDPVNNSVGIYLDTINIFIRIATILAGG +>Pg1Pg2_ContigI_3254 +ERAMAPAGDGAFTLGKGMLAGVSAVGLGMLCYYGLGMSNEVGAIDRAAIWPNVVRQRVKDTYMYFGGSLVFTAAAAVAASRSPMVMRLVMRNGWLALIGTMAAMIGSGMVVRALPYKEGFGSKQMAWIVHSGIVGAVIAPLTLLGGPLMIRAACYTAGVVGGLSALAMCAPSDKFLYMGGPLAMGLGVVIVSSIGGMFIPPTTALGAGMYSVALYGGLALFGMFLLYDTQKIIHRAENHPVYAMQPYDPINNSVGIYLDTINIFIRIATILAGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_53.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>PsIsotig04438_00541_1468 +SWLLGKWRSEDGQGIYPTIKDFKYIEELEFFQVGQPNIQFNFYAFNAETKKPMHREVGFIRVTPDLSKVALVSAQNTGLADIEEGTYNDKEKELRVESCALGRMSFGKLPETKIARIFR +>Ac19848_1/1_1.000_822 +SWLLGKWRSEEGAGHYPTIKDFKYIEEVEFFQVGQPNIQFSFYAFNAETKKPMHREVGFIRVKPDLSKVAFISAQNTGLAEVEEGTYNDKDKELRFESHTIGRLTFGKPPETKIARIFR +>Pf5916_1/1_1.000_798 +SWLLGKWRSEDGHGHYPTIKDFKYIEELEFFHVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFVSAQNTGLAEVEEGTYNDKEKELRFESHTVGRLTFGKPPETKIARIFR +>Pg1Pg2_ContigI_2557 +SWLLGKWRSEDGQGHYPTIKDFKYIEELEFIQVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFISAQNTGLAEVEEGTYNEKEKELRFESHTVGRLTFGKPPVTKIARIFR +>Ap4677_1/1_1.000_1142 +SWLLGKWRSEEGAGHYPTIKDFKYIEEVEFFQVGQPNIQFSFYAFNAETKKPMHREVGFIRVKPDLSKVAFISAQNTGLAEVEEGTYNDKDKELRFESHTIGRLTFGKPPETKITRIFR +>Pp_619_3/4_0.500_1588 +SWLLGKWRSEDGSGQYPTIKGFKYIEELEFFHVGQPNIQFSFYAFNAETKKPMHREVGFIRVTPDLSKVAFVSAQSTGLAEVEEGTYNDKEKELKFESHTVGRLTFGKPPVTKIARIFR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_57.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pp_4624_1/1_1.000_408 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHILYLGGVYRGGHDVLVRAKLALTDSGVTMQITVRSTDSSAAEVIASAVG +>Ap20_1/1_1.000_3490 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVYRGGHDVLVRAKLALTESGVTMQITVRSTDASAAEVIASAVG +>Pf2182_1/1_1.000_391 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRAKLALTDNGVTMQITVRSTDSSAAEVIARAVG +>Pg1Pg2_ContigI_4321 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRSKLALTENGVTMQITVRSTDSSAAEVIARAVG +>Ac769_1/1_1.000_3492 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVYRGGHDVLVRAKLALTESGVTMQITVRSTDASAAEVIASAVG +>PsIsotig22043_14588_2117 +NELEDTYALSSMKTLEEAVKNVIQFMGMQPCERSDKVPEGKSSHTLYLGGVFRGGHDVLVRAKLALSENGVTMQITVRSTDASAAEVIARAVG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_58.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>Pf3163_1/1_1.000_300 +SSSDSDSHSRSSSSDSSSSSGSSSSGTSRSSSSSSSSSSKSRSRGRNRSVSRGR +>Ac5819_1/1_1.000_1087 +SSTDSDSHSRSSSSDSSSSSGSSSSGSSRSSSTSSSSSSKSRGRARNRSISRGR +>Pp_5864_1/2_1.000_1207 +SSSDSDSHSRSSSSDSSSSSGSSSSGSSRSSSSSSSTSSKSRNRGRNRSASRGR +>Pg1Pg2_ContigI_943 +SSSDSDSHTRSSSSDSSSSSGSSSSGSSRSSSSSSSTSSKSRSRGRNRSPSRGH +>Ap10018_1/1_1.000_1141 +SSSDSDSHSRSSSSDSSSSSGSSSSGSSRSSSTSSSSSSKSRGRARNRSISRGR +>PsIsotig05647_00837_2779 +SSSDSDSHSRSSSSDSSSSSGSSSSGTSRSSSSSSSSSSKSRSRGRNRSVSRGR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_aa/locus_6sp_60.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,12 @@ +>PsIsotig13857_06402_734 +ERFFGGGARRNDFSISDCLVTAENSSS +>Ap1982_1/2_1.000_2775 +ERFFGGGALRKDFSISDCLVTAENSSS +>Pp_26038_1/1_1.000_265 +ERFFGGGALRKDFSISDCLVTAENSSS +>Ac6601_1/2_1.000_1710 +ERFFGGGALRKDFSISDCLVTAENSSS +>Pg1Pg2_ContigI_6747 +DRFFGGGARRKDFNISDCLGTAENSSS +>Pf3398_1/1_1.000_178 +ERFFGGGARRNDFSISDCLVTAENSSS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_109_with_3_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,6 @@ +>Lf38763_1/1_1.000_387 +aaggccttgcgccggaacattgcggtgaactgctcgctgatgcgcttgaagagttcctggatggccgtgctgttgccgatgaaagtgccagacatcttgaggccgcgcggcgggatgtcgcagacagcggtcttgacgttgttcgggatccactcgacgaag +>Bj1919_1/1_1.000_456 +aaggccttacgacggaacatggcagtgaactgctcactgatgcgcttgaacagctcttggatggcggtgctgttgccgatgaaggtgcctgacatcttgaggccacgtggtgggatgtcacagacggctgtcttgacattgttgggaatccattcaacgaag +>Bs30874_1/1_1.000_304 +aaggccttgcggcggaacatggcagtgaattgctcagagatgcgcttgaagagctcttggatggcagtgctgttaccgacaaatgtaccggacatcttgaggccacgaggagggatgtcacaaacagcagtcttgacattgttggggatccattcgacgaag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_113_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bs16883_1/1_1.000_765 +caggagttcaaagaagccttcacaatgattgaccagaacagagacggcttcattgacgagagtgacctggcctccatgttccagcagaccggtcgcgaggctgagcccaaacagctgaaggagatgttggctgaggctcccggcacgctcaactttactaacttcctcacgctcttcggcgagaagctgcacggaactgaccccgagaggaccctgcttgatgccttcaagatgttcgacgttgaacgcaagggtatcctgtctgaagaatacctgaaggacctcctggtgaacgttggtgaccagttctccaaggatgagatcaaacaaacatgg +>Lf12022_1/1_1.000_613 +caggagttcaaggaggcgttcacgatgatcgaccagaaccgggacggcttcatcgacgagaacgacctggccgccatgttccagcagaccggacgcgaggctgagcccaagcaactgagagagatgttggccgaggcgccagggaccctcaacttcaccaacttcctcaccttgttcggcgaaaaacttcacgggactgacagcgagcgcaccctgacagacgccttcaagatgtttgacgaggccgggaaaggttacatttcagaggagtaccttaaggacctcctggttaacgttggtgaccagtactctaaggatgagattaaacagacgtgg +>Ha10806_1/1_1.000_456 +caggagttcaaggaagccttcaccatgatcgaccagaacagagatggcttcatcgatgagaacgacctggcttctatgttccaacagaccggtcgtgaggctgaacccaagcagctgaaggaaatgctggccgaggcgcccggcacgctcaacttcactaacttcctcaccttgttcggtgagaagttgcacggtactgacccggagaggacgctcctcgatgccttcaagatgttcgatccggaaggcaaaggggtcctggcggaagaatacttaaagactctcctggtggaagttggtgaccagttctccaaggacgagatcaaacagacgtgg +>Bj297_1/1_1.000_561 +caggagttcaaggaagccttcaccatgatcgacacgaaccgtgacggttttattgacgagtctgatctcgctgctatgtttcagcagaccggtaaggaagccgacccgaaaacgctgaaggagatgattgctgaggcacctggaaccttgaatttcaccaatttcctcacactctttggtgagaagcttcatggaaccgactctgagcgcaccctcattgacgccttcaagatgtttgacgatgagggcaagggtgtgctagcggaagattacctcaaggacctactggtggaggttggtgaccagtttaacaaggatgagcttaagcagacgtgg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_253_with_2_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,4 @@ +>Ha10499_1/1_1.000_784 +ttctggatcagctgggatcgtggcctggtgcgagtcggggagggcacgcgccgcaaccaccagcccttcctcgtgtggaacgtccccgagaacaagcagcacggggtcaactgcatcgccgtctcctccgggcctgggtcggagggcgagtgggagttc +>Bj32890_1/1_1.000_2739 +ttctgggtgagctgggaccgcggctcggtgcgggttggcgaggggtcgcgccgcactcaccagcccttcctggtgtggaacgtgcccgagaacaagcagcacagcgtcaactgcatagcagtctcctccgggcccggctccgagggcgagtgggagttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_283_with_2_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,4 @@ +>Ha1337_1/1_1.000_1215 +gacttcttgatcttctcttcgaacagatcctttttgttgaggaaaagaatgatagaggtatcggtgaaccatttgttgttacagatcgagtcgaacagcttc +>Bs2095_1/1_1.000_1167 +gacttcttgatcttctcttcgaataaatccttcttattaaggaagagaataatagaggtgtccgtgaaccatttgttattacaaatagagtcgaacagcttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_299_with_2_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,4 @@ +>Bj17018_1/1_1.000_567 +tgcttcccgtccaaccaggaagttttctcggtacagatgaaaaactgtgatccgtttgtgttagggccagcgttcgccatcgacagcataccaggccctgtgtgcttcaaagtgaaattttcatcagcaaac +>Bs1426_1/1_1.000_513 +tgcttcccgtccagccagtcggtcttgacggtacagaggaagaactgcgacccgttggtgttggggccggcgttggccatggagaggataccgggtccagtgtgctttagggtgaagttctcgtcagcgaac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_301_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Ha10118_1/1_1.000_897 +gaggatgatgaggaacaggtagacgatgtccaagtagagctgcagcgctccgaacacgtggtcctccggggacagctcgaacttcttgcctccgatcagcatctgtgtgtcgtaagccaggaacatggagaa +>Lf311_1/1_1.000_384 +gaggatgatgagaaagaggtagatgatgtcgaggtagagctgaagtgctccgaacacgtggtcctctggcgacagtcggtacttcttgttgcccatcagcatctgggtgtcatacgccaggaacatagagaa +>Bs27070_1/1_1.000_699 +gaggatgatgatgaagaggtagacgatgtccaggtacagctggagcgcaccgaacacgtgatcctccggggagagctcatgcttcttaccgccaaccagcatctgggtgtcgtacgccaggaacatagagaa +>Bj17798_1/1_1.000_1215 +gaggaagatgaggaagaggtagactatgtccaggtacagctggagcgcaccgaacacatggtcctctggggagagctcatacttcttaccgccaatcagcatctgggtgtcatatgcgaggaacatagagaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_316_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bs27803_1/1_1.000_1664 +gtgaacgcgccccctgtcccctcctctcgcgacactgcgctcaccatcgccgcagacaagggccactaccgctttgtggaactgctcctctccagaagcgctgccgtagacgtgaagaacaagaaggggaactctcctctgtggttggcttgcaacggtgggcacctggatgtggtgcagttactcgtgaacgccaaggcggatatcgacagccaggacaaccgcaaggtgtcgtgcctcatcgcggccttccgcaaaggtcacgtgaaggttatcaaatggatggtgaagcatgtggcacagttcccttcggaccaggagtgcatgcgatacatctcaaccatcacggataaggagctgctgaaaaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaggcagcggaggcgaaccggcacgcctctatcctcctggaacagttggaccgcgagaagagcctggaggagagcaagaaggcggccgcagcccgcaagcgcgagaagcgacgccggaagaagaaggagaagcaggagcaggcgaacaacaaaaaccaggcacacaagcgaagtcggaacactgaggtgagctcgaacagcagcagtagcagcgagtcgaatggcaagacgaagagcaagaagagcaagaaggccgagcgc +>Bj26780_1/1_1.000_2698 +gtgaatgcgccccccgttccctcctctcgcgacactgcgctcaccattgccgcagacaagggccactatcgctttgtggagctgctcctctcgagaagtgcggccgtagacgtaaagaacaaaaaggggaactctcctctatggttggcttgcaacggtgggcacttggacgtcgtgcagttattagtgaacgccaaggctgacattgacagtcaggacaaccgcaaggtatcatgcctcattgcggctttccgcaaaggtcacgtcaaggtgatcaaatggatggtgaagcacgtggcacagttcccttcagaccaggagtgcatgcgatacatctcaaccattacggacaaggagctgctgaaaaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaggcagcggaggctaaccgccacgcttccattctcctggagcagctggaccgtgagaagagcttagaggagagcaagaaggcagcggccgcccgcaagagggagaaacgacgccgcaagaagaaggagaagcaggaacaggcgaacaacaaaaaccaggcgcacaagcggagtcgtaacaccgaggtgagctcgaacagcagcagtagcagcgaatcaaatggcaagacgaagagtaagaagagcaagaaggctgagcgc +>Ha1883_1/1_1.000_5577 +gtgaacgcgccacccgtgccctcttcacgtgacaccgccctcaccatcgccgcagacaagggccactaccgcttcgtcgagctgctcctctcccgcagtgctgccgttgatgttaagaacaagaagggcaactcgccgctctggttagcctgcaacgggggtcacctggatgtggtgcagctgttggtgaatgctaaggcagacatcgacagtcaggacaaccgtaaggtgtcgtgcctcatcgccgccttccgtaaggggcatgtcaaggtcatcaagtggatggtgaagcatgtggcccagttcccgtcagaccccgagtgcatgcgctacatctcgaccatcactgacaaggagctgctgaagaaatgccaccagtgcatggagattatcgtcagtgccaaggaccggcaagcagccgaggccaaccgccacgcatctatcctactagagcagctcgaccgagagaagagcctagaggagagcaagaaagccgccgcagcccgcaagagggagaagcggcggcgaaagaagaaggagaaacaggagcaggcaaataacaaaaaccaagcccacaagcggagtcgcaatttggaagtgagcagcaatagtagcagtagcagcgagtccaacggcaagaccaagagcaagaagagcaaaaaggccgagcgg +>Lf1892_1/1_1.000_9654 +gtgaacgcgccgcctgtgccgtcatcccgcgacaccgcgctcaccatcgccgctgacaaggggcactaccgctttgtggagctgcttctctccaggagtgctgctgtggatgtaaagaacaagaagggaaactctcctctctggctggcctgtaatggtgggcacctggacgtggtgcaattattggtgaacgccaaggcggacatcgacagccaggacaaccgcaaggtgtcgtgtctgattgcagctttccgcaaaggtcatgtgaaggtcatcaagtggatggtgaagcatgtggcccagttcccgtcggaccaggagtgcatgcgctacatctcgaccatcacagataaggagctgcttaagaaatgccatcaatgcatggagatcattgtgagcgccaaggaccggcaagcagcagaggcgaaccggcatgcgtcaattctcctggagcagctcgaccgcgagaagagtctggaggagagtaagaaggccgcagccgcccgcaagcgggagaaacgtcggcggaagaagaaggagaagcaggaacaggcaaacaacaaaaaccaggcccacaaacgaagtcgtaacactgaggtgagctccaacagtagcagcagcagcgagtcaaacggcaagaccaagagcaagaaaagcaagaaggcggagcgg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_335_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Lf1038_1/1_1.000_963 +gcgccgcatggcgacggtcgagtagttgcagtgcgcgccagcgccgttccagtctcccggcatcggcttcgggtcgaagctgacgacgatcccgaagtcctcagcgacacggtgcaggacgtagcgcgccatccacaggtcgtcgcccatctggatgccctcacacggacccacctggaactcccactgtcccggcatcacctcggcgttcgtgccggcgatcttgatgtcggcgta +>Bs16552_1/1_1.000_1152 +ctccctcatggccagcgtcgagaagttggtgtgtgccccggcaccgttccagtctccgggcattggcttggggtcgaaactgacgacgatgccaaagtcttcggcgactctgtgcaggatgaatctggccatccagaggtggtcgcccatgctgattccctcacagggtcccacttggaactcccactgggcaggcatcacctcagcgttggtaccggcgatcttgacgccggcgta +>Bj389_1/1_1.000_1311 +ttctctcatggcttgtgtggagtagttggtgtgtgcacctgcgccgttccagtctccgggcatgggtttggggtcaaaggtgacgatgactccgaagtcctctgcgactctatgcagcaagtagcgggccatccagaggtggtctcccatctcaatgcccaggcacgggccaacctggaactcccactggccgggcatgacctcggcgttggttccggctattttgactcctgcgta +>Ha2081_1/1_1.000_1176 +ctccctcatggccttggtggagtagtttgtgtgtgcaccggcaccattccagtctccgggcatgggtttggggtcgaaggtgacgatgacaccgaagtcctctgctacacggtgcagcaggtagcgggacatccacaggtggtcgcccatgtcgatacccaggcacggccctacctggaactcccactgggcaggcatgacctcagcattagtaccagagatgttgacccctgcgtg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_343_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Ha10325_1/1_1.000_531 +ccccgtactgggtgccccacgctgaccgcatccactacatctctaaggactgtgagagggactggttcaacgactgggagtgtatggagtgctgcaacggagatctctgcaactactatgtca +>Bs3268_1/1_1.000_471 +ccccctactgggtgccccacgctgaccgcatctactacatctccaagaactgcgagcgcgactggttcaacgactgggagtgcatggagtgttgcaacggcgacctgtgcaactactacgtca +>Lf56088_1/1_1.000_447 +ccccttactgggtgccctacggagaccgcgcctacttcgtctccaagaactgcgagcgcgactggttcgacgactggggctgtgtggagtgctgctcgggcgacctgtgcaactactacgtca +>Bj5017_1/1_1.000_456 +ccccctactgggtgccccatgctgaccgcatctactacatctccaagaactgcgagcgggactggttcaacgactgggagtgcatggagtgttgtaacggcgacctgtgtaactactacgtca
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_368_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Lf51152_1/1_1.000_999 +aggcggatggtgtttgagaagaacatgatgttcatccgagaccacaacatggaggctgaccttggacacaagtccttccgggttggggtcaagaaccaggcacaatgtggatcctgctgggcgttctccgccattggggccctggaaggtcaacacttcaggaagacaggggatctcgtctctctatctgagcagaacctggtcgactgctcaacaacagaagga +>Ha12847_1/1_1.000_855 +aggcggatgatcttcgagaagaacatgaacttcatccgtgaacacaacatggcagctgatcttggccacaagaccttccgtgtcggtgtcaagaaccagatgcaatgtggatcatgctgggccttctccgctactggctcccttgaaggtcaacatttcaagaagacaggaaagctggtctccctttcagaacagaatcttgttgactgttcccaagctgaagga +>Bs1045_1/1_1.000_633 +aggcgaatggtgttcgagaagaacatgatgttcatccgggaccacaacatggaagctgaccttgggcacaaatccttccgggtcggagtcaagaaccaggaacaatgtggttcctgctgggccttctctgcaactggctcactggaggggcagcacttcaagaagacaggcaagcttgtctccctgtcagagcagaacctggttgactgctcccaggccgaagga +>Bj108003_1/1_1.000_523 +aggcgaatggtgtttgagaagaacatgatgttcatccaggaccacaacatggaggctgacctggggcacaagtccttccgggttggaatcaagaaccagggggcttgtggctcctgctgggctttctctgcaactgggtcgctcgagggacagcacttcaagaagactggtaaccttgtctccctgtcagaacagaacctggttgactgttctaaggctgaagga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_404_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Lf14756_1/1_1.000_456 +gtcagcctttccatcacggttgctgtcaagtttgtcggcgagtccgtctttgttctggtc +>Ha5212_1/1_1.000_491 +gtcctccttgccatcacggttgctgtccagcttgtcagctactccatcgttgttctggtc +>Bj16996_1/1_1.000_378 +gtccttcttgccatcacggttgctgtcaaatttgtctgcgagcccatcgttgttttggtc +>Bs10543_1/1_1.000_387 +gtccttcttgccatcgcggttgctgtcaagcttgtcagcgagcccatcgttgttctggtc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_442_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj29526_1/1_1.000_478 +acacacaatgaaggagttggcatctccagcatagtagaagccataattatagccagaagcgcagtcaccctcaaaatgtccgaggtagtaaaactggccagctccaacatgaactgggtaggctcccaaagtgcggtagttgaactcattgttgaaaccaaatccttctccatatccata +>Bs16935_1/1_1.000_456 +acatacgatgaaggagttggcatctccagcatagtagaatccatagttgtagccagaggcgcaatcaccattgaaatgtccaaggtagtagaactggccagctccaacatgaactgggtaggctccaaaggtacgatagttgaactcattgttgtagccaaatcctactccatatccata +>Ha22482_1/1_1.000_398 +acacacaatgaaggagtcagcatttccagcaaagtagaagccataattgtatccaccagcacagttaccattgaactgcccaaggtagtagaactggccatttcctacatgaactgggtaggcaccaaatcctcggtagttgtactcattgttgaagccataccctactccagcaccaga +>Lf10136_1/1_1.000_570 +gcacacgatgaaggagttagcatcctcagtgtagtagaagccgtaattgtagccattggcgcagttaccattgaagtttccaaggaaatagaactgcccagctgcaatattgaaaggatatgctccgaatccatgatagttgaactcattgttatagccatatcctactccatatccata
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_487_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj104219_1/1_1.000_544 +ggcttctgggacaagttgatccttgagccttacggccggcagcgggacatagtctac +>Lf26378_1/1_1.000_6633 +ggcttctgggacaagctgatactggaaccatacggccggcagcgagacattgtctac +>Ha278_1/1_1.000_2763 +ggcttctgggacaagttgatcctggagccgtacgggcggcagcgtgacgtggcctac +>Bs54896_1/1_1.000_618 +ggtttctgggacaagctgatccttgagccttatgggcggcagcgggacatcgtctac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_508_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj115168_1/1_1.000_390 +tcctcctcctcctccgagctgctgacgtcaccaaatatgtcttcctccaggaatttgctaatgttctccgatgcggctgcgttctcgaccttcttggcctccgatgagttcagtggattgaacacgtccccg +>Lf36714_1/1_1.000_1599 +tcctcctcttcctcggagctgctcacgtcgccgaagatatcctcctccaggaatttgctgatgttctccgaggcggctgcgttctccaccttcttagcttcggaggaattcagcgggttgaaaacatcgccg +>Bs6083_1/1_1.000_337 +tcctcttcctcctcagagctgctcacatcaccaaagatatcctcctccaggaatttgctgatgttctccgacgcggctgcgttctcgaccttcttggcttcagatgagttgagcgggttgaacacatccccg +>Ha18272_1/1_1.000_681 +tcctcctcctcttctgagctgctcacgtcgccgaagatatcctcctctaagaatttgcttatgttttcagaggcggcagcattttccactttcttggcctctgatgagttaagtgggttgaagacgtctccg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_544_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj19203_1/1_1.000_2676 +gaactgaagcgagcagacttcaagctgatcggcaagggcaagtctgacccctactgcaagatctacatcgggtcccagatgtacaagacacgagtgatcgaaaacaccattaacccagtctggaacagctacttcgaggcggttgttgaccaaaaacatggccaatttgcggagcttgaggtacttgaccaggatcctggggaggatgacgaactgggaacggcaagtattgatattgagaacgtggcagtaaagggctcattggacacgtggctccctcttgagaatgtcgagaccggcatggtgcacatccgggcaatatggcttcacctcagcaagaaccctaaagacctg +>Lf110082_1/1_1.000_1416 +gaactgaagagagccgacttcaaactggtcggcaagggcaagtccgacccctactgcaagatctacatcggtgctcagatgtacaagacgaaggtaattgagaacacgatcaacccggtctggaacagctacttcgaggcggttgttgaccagaagcacggtcaatttgcggagctcgaggtacttgacaaagatccgggtgatgatgacgagttgggcacagcgagtatcgacatcgagaatgttggcgacaagggcacattggacacgtggctgccgctggagaacgtggagacgggtatggtacacatccgtgccatatggctgcacctgagtaaggacccggccgacctg +>Ha37107_1/1_1.000_642 +gaactgaagcgggccgacttcaaactggtggggaaaggcaaatcggacccctactgcaaaatatacattggcgcacagagcttcaagaccaaagtgatagaaaacactatcaatcctgtatggaacagctactttgaggcggtagtggaccagaagcatggacaattcgctgaactggaagtgctcgatcaggatcctggagaagatgacgaacttggaacggcgagtgtggacatccagaatgtaggtgaacatggctcaattgacacgtggctccccctggagaatgtggacactggcatggtgcacatccgtgctatgtggctgcacctgagtaaggaccccgctgatctg +>Bs13030_1/1_1.000_2652 +gaactgaaacgggcagacttcaaactggtcgggaagggcaagtcggacccctactgcaagatctacatcggcgcccagatgtacaagacgaaagtcatcgaaaacaccattaacccagtctggaacagctacttcgaggcggttgttgaccaaaaacatggtcaatttgcggagcttgaggtacttgaccaggatcccggtgaagatgacgaactgggcacagcaagtattgacattgaggacgtgggtgcaaaaggctcactggacacgtggcttcccctggagaacatcgaaactggcatggtgcacgtccgggccatctggctccacctcagcaaggacccgaacgacctg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_546_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Ha41649_1/1_1.000_527 +ctcaccccggtacctgtagacgaacccgctcacacctgtacactacattcacgctacacctgcctcattaag +>Lf11086_1/1_1.000_2517 +ctcaccccagtacctgtggacgagccggcacacacgtgcaccctccatgcacgctacacgtgtctcgtgaag +>Bs41282_1/1_1.000_485 +ctgagcccggtgcctgaagacgagccagcacacacatgcactctgcatgcacgctacacgtgcctggtgaag +>Bj19624_1/1_1.000_1584 +ctgagcccggtgcctgtagacgagcctgcccacacgtgcacccttcatgcacgctacacgtgtctggtgaag
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_588_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj3220_1/1_1.000_3147 +agtttggagaccgagtgcccgccgacgtgcgcgttagctcatggatttaaggtggacaactcctcgctgactggggaatctgagcctcagactagaaccgcagagttcacgaatgataacccgctcgagaccaagaacctcgccttcttctcaacaaatgctgttgaaggcacgtgtcgcgggattgtagtgagcactggggaccgcaccgttatgggccggatcgccaacctggcatccggactcgagatgggccagactccgatcgcacgtgagatcgaacatttcatccacatcattactggtgtcgctgtattcctcggcgtagccttctttatcgtcgctttcatccttggttactactggcttgatgctgtcatcttcctcatcggtatcattgtcgccaatgtgcccgaaggtctgctggctaccgtcacggtgtgcctgactctgaccgctaagcgcatggcgtccaagaactgtctcgttaagaacctggaggccgtggaaacacttggctccacatccacaatctgctccgataaaacgggaactctcactcagaaccgtatgactgtcgctcacatgtggttcgacaaccgcatcattgaggcggacaccactgaggatcagtcagcagatgcgggctgtgacgcggcatctgccacttggcaaagtttggcgcgtattgccatgttatgtaaccgcgctgagttcaagatgggacaggagaaccttcctgtactaaaaagggaatgtaacggcgacgcctccgagtctgcgctgctgaagtgcgcagagctatctatcggcaaggtgagagagttccgcgcaaagcacaagaaagcagttgaaattccattcaactcaaccaataaatatcaggtctctgtgcatgagatgccggacgatccgcgctacctgcttgtaatgaagggcgcccctgagcgcatcctggaccgctgcactaccatcctcattaatggcgaagagaaacccgtgtctcccgagtggaaggaggccttcgaacattcctacatggagttgggaggccttggagagcgcgtactcggattctgtgactacatccttgatgttgcaaaattcccacgtggctatccgtttgactcggaggaagagaacttccccctgaccggcctgcgcttcgttggtcttatgtccatgatcgaccctccacgagccgccgtgccggatgccgtgggcaaatgtcgcagtgctgggattaaggtgatcatggtgacgggcgaccatcccatcaccgccaaggccatcgcgaagggcgttggcatcatctctgagggaaatgaaactgtagaggacatcgctgcacggctcaacatacccgtcagtgaagtcaaccccagggacgctatggcatgtgttgtacacggctctgacctgcgtgatatgacccctgctcaaatagacgacatcctcagcaaccacacggagattgtattggcacgtacttcaccgcaacagaaactcatcattgtcgagggctgccaacgtcaaggcgccattgttgctgtcacaggcgatggggttaacgactcccctgccctaaagaaagccgatatcggagttgccatgggcattgctggcagcgacgtgtcgaaacaagcggctgacatgattcttctcgacgacaacttcgcatctattgtaactggtgtagaagagggccgtctgatcttcgacaacctcaagaagtcgatcgcctacaccctcacctcgaacatccccgaaatctctcccttccttctcttcatcctggccgatgtgccactgcccctgggaaccatcaccatcctgtgcattgatctcgggaccgaccttgtcccagcgatctccttggcctacgagcaggctgaaagtgacatcatgaaacgccagccccgtgatcctctccacgacaagctcgtgaacaacaggctgatcggcatggcctacgggcaggtcggtatgatccaggcatcggccgggttcttcgtctacttcgtcatcctcgccgagaatggcttcttgccatcacggcttctcggcatccgggaaagttgggactcgaaggctatcaacgacgagctcttatggtcaggagtggacatacgcccagcg +>Bs118_1/1_1.000_3114 +agttcggggaccgggtgcctgccgacgtgcgtgtcagcgcacggcttcaaggtggacaactcctccctgaccggagagtccgagcctcagacgaggaccgccgagtttactaacgacaacccgctcgagactaagaatctcgccttcttctccacgaatgctgttgaaggcacgtgccgcggcgtcgtggtgagcacgggtgaccgcacggtgatggggcgcatcgccaacctggcctccgggctcgagatgggccagacgccgatcgcgcgcgagatcgaacacttcatccacatcatcacgggcgtggccgtgttcctcggcgtcgccttcttcatcgtcgccttcatcctcggctactactggctcgacgcagtcatcttccttatcggaatcattgtcgcgaacgtgcccgaaggtctgctggccaccgtcacggtgtgcctgactctgaccgctaagcgcatggcgtcgaagaactgcctcgtcaagaacctggaggctgtcgaaactctgggctccacgtccaccatctgttctgacaagaccggaaccctcacccagaaccgaatgactgtcgcccatatgtggttcgacaaccgcatcgtcgaagccgacaccactgaggaccagtcagcagatgcatgctacgactccaagtctgccacatggatatgtctggcgcgtattgccatgttgtgtaaccgcgccgagttcaaaatgggacaagagaatgtccccgtactgaagagagagtgtaacggtgatgcctcggaatctgcgctgctcaaatgtgtcgaactgtccatcggtaaggtgaccgagttccgtgccaaacacaagaaggctgtagaaattccattcaactcaaccaacaaataccaggtatccgtgcacgagatccctgacgacccgcgctacctgctcgtcatgaagggcgcccccgagcgcatcctcgaccgctgctccaccatcctcatcaacggcgaagagaagccgatgagcgaagactggaaggaagcctttgaacaatcctatatggagctcggagggcttggcgagcgcgtccttggattctgcgactacatcctcgatgctgcacagtacccccatggctatcccttcgactccgaagaggagaacttccccctgaccggtctgcgctttgtgggtctcatgtcgatgatcgaccctccacgtgccgctgtgcctgatgccgtgggaaaatgtcgcagcgctggaattaaagtgatcatggtgactggtgatcatcctatcactgccaaggctattgccaaaggtgtcggaatcatctccgaaggcaatgaaactgtcgaagacatcgctgcacgcctcaatattcctgtgagcgaagtcaaccctagagatgccaaggcttgcgttgtccatggctccgacctgcgcgatatgacgccagcacaaattgatgacatcctcgttaatcacattgagatcgtgttcgcacgaacctcacctcagcagaaactcatcattgtcgagggctgccaacgtcaaggcgccattgtcgctgtcaccggtgacggcgtcaatgattcacccgcgcttaaaaaagccgacataggcgttgccatgggcattgctggcagcgacgtgtcgaaacaagcggccgacatgatcctgctcgacgacaactttgcctccatcgtcactggtgtcgaagaaggtcgtctgatcttcgacaacctgaagaagtcgatcgcctacaccctgacctcgaacatccctgaaatctcgcccttcctcctcttcatcttggccgacgtgcccctgcccctgggaaccatcaccatcctgtgtattgatctcgggaccgaccttgtccccgccatctccttggcctacgaacaggctgagagcgacattatgaaacgccagccccgtgatcctctccacgacaagctcgtgaatcacaggctgatcggcatggcctatgggcagatcggcatgatccaggcctcggccggcttcttcgtctacttcgtcatcctcgctgagaacggcttctggccgtcgcatctgcttggtctgcgcaagcgttgggattccaaagccgtgaatgacgagctcctatggacaggagtggacatatgcccaacg +>Ha3202_1/1_1.000_3108 +agttcggggacagggttccggctgacgtgcgtgtcagcacacggtttcaaggtcgacaactcctccctgactggtgaatccgagccgcagacaagaactgctgagttcaccaacgaaaaccctctagaaaccaagaacctggcattcttctcaaccaatgccgtcgaaggtacctgccgtggtgttgtcatcagcaccggtgacagtaccgtcatgggccgtattgccaacctggcctccggtctcgagatgggccagactccgattgcccgcgagatcgagcatttcatccacatcattactggggtagccgtcttcctgggcatatcattctttgtcatcgccttcatcctcggctattactggctcgatgccgtcatcttccttatcggtatcatcgtcgccaacgtgcccgaaggtctgctcgccaccgtcacggtgtgcctgaccctgactgccaagcgtatggcgtccaagaactgtctggtgaagaacctggaagccgtggagaccctcggctccacctccaccatctgctccgacaagaccggcacactcacccagaaccgtatgaccgtcgcccacatgtggttcgacaaccgcatcgtcgaggctgacaccactgaggaccagtcagcagacgcatgctacgactcctcctccccgacttggttggccctggcctgcatcgctatgctctgtaaccgtgctgagttcaagatgggccaagaatctgtacctgtactaaagagggaatgtaacggtgatgcctcggagtccgctctgctgaagtgcgttgagctgtccatcgggaaggtggtcgagttccgtgccaggcacaagaaggccgtagaaattccattcaactcaaccaacaaataccaggtgtctgtacacgaggtaccagatgatcctcgctacctgctggtgatgaagggagcccccgagcgtatcctggaccgctgctccactatcctgatcaacggcgaggagaagcccctctcggatgagtggagggaggccttcaaccaggcctacctcgagttgggaggcctcggagagcgtgtgcttggattctgtgactactaccttgacgccgctcagtacccccatggctaccccttcgactctgaggaagaaaacttccctctaactggactccgcttcgtcgggcttatgtccatgattgaccccccacgtgctgctgtgcctgatgctgtcggcaaatgccgcagcgcaggcatcaaagttatcatggttaccggcgaccaccccatcactgccaaggctatcgccaaaggtgtcggaattatctccgagggcaacgagaccgtggaagacatcgctgccaggcttaacattcccgtcagcgaagtcaacccaagggatgcgaaggcttgcgttgttcacgggtccgacctacgcgatatgaccccggctcagattgatgatatcctcgccaaccacaccgaaatcgtgtttgcacgtacctcaccccagcagaaactcatcattgtagaaggttgccagcgccaaggagccattgtggctgtcactggtgacggtgtgaacgactcaccggccctcaagaaggctgacatcggtgttgccatgggcatcgctggtagcgacgtgtccaaacaggccgccgacatgattctgctggatgacaacttcgcctctattgttacaggcgtggaggaggggcgtctgatctttgacaacctgaagaaatcgatcgcctacactctgacctcgaacatcccagagatctcccccttcctcctcttcatcctggctgacgtcccacttcctctcggaactatcaccatcctgtgtattgatctcgggaccgaccttgtccctgctatctcccttgcctacgagcaggcggagagcgatattatgaagcgccagccccgtgatcctcttcacgacaagctcgtgaaccacaggctgatcggcatggcttatggccaaattggcatgattcaggccactgccggcttcttcgtttacttcgtcatcttggccgagaatggcttctggccatcccgtcttctcggcatccggatgcgttgggattcgaaagcggtgaacgacgagctcctatggacaggagtggacctacgcccagcg +>Lf11686_1/1_1.000_3102 +agttcggggaccgcgtcccggccgacgtcagggtcagcccacggctttaaggttgacaactcatcactgaccggagaatctgaacctcagtcaagaactgccgagtttaccaacgagaatccactcgagaccaagaaccttgctttcttctccacgaatgctgttgaaggtacgtgccgtggcgtcgtggtcggcacgggggaccgcaccgttatggggcggattgcaaacctggcgtctggcctcgaagttggtcagactccaatcgcacgagagatcgagcatttcatccacatcatcacgggcgtggccgtgttcctcggtgtcgccttcttcatcgtcgccttcatccttggctactactggctcgatgcagtcatcttcctcattggtatcattgtcgctaatgtccccgaaggtctgcttgctactgtcacagtatgcctgacactgaccgccaagcgcatggcgtccaagaactgtctcgttaagaaccttgaggctgtcgagacgctcggatctacctccaccatctgctccgacaagactggcaccctcacccagaaccgcatgacggtcgcccacatgtggttcgacaaccacatcgtggaagccgacacgaccgaagaccagtccacggaggccgggtgcgactctgcatcccccacatggcagtgtctgatccgcgttgctatgttatgtaaccgtgccgagttcaaaatgggacaagataaattccctgtactgaaaagggaatgtaatggcgatgcttctgaatctgccttgttgaagtgtgccgaactctccattggcaaagtaattgagttccgtgccaaacacaagaaagccattgaaattcccttcaactcaaccaacaaatatcaggtgtctatacatgagctgccagatgacccacgctacctgctcgtaatgaagggcgcccctgagcgcatcctggaccgttgtgccaccatcctcataaatggggaggagaagccgatgagtgaggaatggaaagaggcatttgagcagtcctacatggagctgggcgggctcggcgagcgcgtgctcggattctgcgacttcattctggatgctgaaaagtttccccggggctatccattcgatgctgacgaggagaacttcccactgacagggctgcgctttgtggggctcatgtcgatgatcgaccccccgcgtgctgctgtcccagacgcggtcggcaaatgccgcagcgctggaatcaaagtcatcatggtaactggggaccacccgatcactgccaaggccatcgctaagggtgttggcattatctctgagggcaatgaaactgtagaggatatcgccgcacggctcaacatacccctcagccaggtcaagcccagtgatgcgaaagcttgtgtcattcatggctctgacctccgtgatatgacacctgctgaaatagatgacatgctccgaaaccacactgaaatagtgatggcgcggacctcgccccagcagaaactcatcattgtggagggctgccagcggcagggcgccattgtagctgtcacgggtgacggtgtgaatgattcacccgccctaaagaaagcagatattggagttgccatgggcatcgctggtagcgacgtgtcaaaacaagcggccgacatgatccttcttgatgacaactttgcatctattgtcactggcgtagaagagggacgtctgatcttcgacaacctgaagaaatcgattgcttacactcttacttcaaacatcccggaaatttccccattccttctgttcatcctggctgatgtgccactgcctctgggaaccatcaccatcctgtgtattgatcttgggacggatctcatccccgccatctcactcgcatacgagcaggctgaaagcgacatcatgaagcgccagccccgtgaccctctccacgacaagctcgtcaacaaccggctcatcggcatggcctatgggcagattggcatgattcaggcctctgccggcttctttgtttactttgtgattcttgcagagaatggctttttaccgtgggatctgtttggcatccgtcaaaactgggattccagggctgtaaacgataagctcctatggacaggagtggacgtacgcccagcg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_623_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj55915_1/1_1.000_1497 +ctggtgcgtctgtcccagcaggagctgatcgactgctcgtggggagaggggaacaatggatgtgatggcggagacgacttcctcgcctaccagtggatttccaaacacggactggcc +>Lf5592_1/1_1.000_1659 +ctggtacggctgtctcagcaggagctaatcgactgttcgtggggagaggggaacaacgggtgtgacgggggtgatgacttccgcgcctacaagtggattactaagcacggactggcc +>Ha1592_1/1_1.000_1710 +ctggtgcgcctgtcccagcaggagctggtagactgttcgtggggtatgggtaacaacgggtgtgatggcggagaggacttccgtgcttaccagtggatcaccaagcacgggctggcc +>Bs34509_1/1_1.000_1086 +ctggtgcgcctgtcacagcaggagctgatcgactgctcgtggggagaagggaacaatgggtgtgacggaggagaggactttcgtgcctaccagtggatcagcaagcacgggctcagc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_651_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bs8968_1/1_1.000_1776 +tgtgaagaggatgcaggaggtctgctgcagactgaatgcctgtcctcctggaagcaggacaacacgacgctggttctcgtccgccgattagacgtcagcaag +>Ha12591_1/1_1.000_492 +tgtgaggaggatgttggaggtctgatgcaaactgaatgtctatcatcgtggaaacaggataacacgacactggtgctggtgcgccgtctcgactcccacaaa +>Lf56294_1/1_1.000_1773 +tgtgagcaggatgctggtggtttactgcagactgagtgcctctccacgtggaaacaggacaacaccacactggttcttgtcaggcgcctagacgtcagcaag +>Bj88046_1/1_1.000_797 +tgtgaggaggatgcgggtggtttgctgcagacagaatgtctctcctcctggaagcaggagaacacgacgctggtgctcgtccgccgtctggacgtcagcaaa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_660_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bj102_1/1_1.000_1566 +gcagatggtatcgtgaagacgatgcgctccaaggcaggccccagctccaaggaacttaaggccgccgacgaggtcgagaagtttatcaatggaaaagatcttgtcatcgttggcttcttcgagtctgatggcagt +>Lf3141_1/1_1.000_1467 +tcagatgggattgtaaagacgatgcgctccaaggcgggacccacatcgatggaattaaaggctgttgacgatgttgagaaatttattggcggaaaaggtcacgtcgttgttggtttcttcaagtcggaaggcagt +>Bs17280_1/1_1.000_360 +gcagatggtattgttaagaccatgcgtggcaaggctggcccaagctccaaggaactcaagtctggtgacgaagttgagaagtacatctcaggaaacgacattgtcttcgttggtttcttcgaggctgagggcagt +>Ha1450_1/1_1.000_1497 +gcagatggtattgttaagaccatgcgtggcaaggctggcccaagctccaaggaactcaagtctggtgacgaagttgagaagtacatctcaggaaacgacattgtcttcgttggtttcttcgaggctgagggcagt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_696_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Lf46816_1/1_1.000_3195 +aagctcaacgcgcagctcctaaaccacccgctcacccaccagcacttcgtccccgcactcatgaagttctacgtcgacattgagacgactggtgcgagtagcgaattctatgacaagttcacggtgcgctaccacacgtccattatcctgaagacgctgtgggaaatccctatgcaccaagcgcgcattgtggaggaggccaccggggcagtttgtccgtttcac +>Bj11264_1/1_1.000_1503 +aagctcaactcacagctcctcaaccacccactgacgcatgagcatttcgtaccagcactcatgaagttctatgtcgacattgagacgacgggtgcaagtagtgagttttacgacaagttcacagtacggtaccacacgtccatcatcctgaagaatatgtgggacatccccatgcaccaggcacgcattgtgaaggaagcgactggggcagtttgtgcgatttac +>Ha2853_1/1_1.000_2274 +aaactcaacactcagctactcaaccacccgctaacacatcaacactttgtacccgcactcatgaagttctacgtagacatagagacgacgggggcgagcagcgagttctatgacaagttcacggtacgctaccacatcagtatcatcctcaagaccatgtgggacatccccatccaccagggccgcatcgtacaagaagccatcgggccagtttgtgcgtttcac +>Bs8429_1/1_1.000_306 +aagctcaactcgcagctcctcaaccacccgctcacacatgagcatttcgtaccggcactcatgaagttctacgtcgacattgagacgacgggggctagtagtgagttctacgacaagttcactgtgcgatatcacacgtccatcatcctgaagaatatgtgggacatccccatgcaccaagcacgcattgtgaaggaggcaactggagcagtttgtgcggtttac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_707_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Ha58565_1/1_1.000_582 +tgtgtaagatctcagactttggcagctcacgggacatcgcacagagccggcagtacgagagccgcacacagaaccggttaccgatacgttggatggcgcctgagtctctgtatgattgcatgtacagtatcaagtctgacgtctggtcctttggggttctactctgggagatcgtcacac +>Lf5218_1/1_1.000_3096 +tgtgtaagatctcggactttggcagcgcgcgggacatcgcgcagagccggcagtatgagagccgcacacagaaccgcctgcccatccggtggatggcgcccgagtcgctgtacgactgtatgtacagcgtcaagtccgacgtgtggtccttcggcgtgctgctgtgggaaattgtcacac +>Bj116010_1/1_1.000_312 +tctgcaagatctctgactttgggagttctcgcgacatcgcacagagccggcagtatgagagtcgaacgcagaaccgccttccaatccggtggatggcgcctgagtcgctgtacgactgcatgtacagcgtcaagtcggacgtctggtccttcggggttctactctgggaggtcgtcacgc +>Bs1374_1/1_1.000_1335 +tgtgcaagatctccgactttggaagttctcgcgacatcgcacagagccgacagtatgaaagccggacgcagaaccgccttccaatccggtggatggcgcctgagtcactgtatgactgcatgtacagcatcaagtcagacgtctggtcctacggcgttctgctgtgggagatcgtcacgc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_727_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Lf1012_1/1_1.000_735 +tatggctgggtctaccgaaatgggcgggacttgtccggcttcatcgacggaactgagaatccggctgacgggagctacgtgattacccaacgatgggttcataacctggcgaagataaagaagacaaaagat +>Ha1000_1/1_1.000_1200 +tacggctgggtgtaccagaatggtcgtgacttgtcagggttcattgatggtactgagaaccctgccgacggaagttacgtgatcacacaacgatgggttcacaacttggagaagatcaagaagactaaagat +>Bs2375_1/1_1.000_555 +tacggctgggtgttccgccaggggcgcgacctgtccggcttcatcgacggcaccgagaacccggcggacggaagttacgtgatcacccagcggtgggtccatgaccttgaaaagattaaaatgacaaaagtg +>Bj12534_1/1_1.000_1269 +tacggctgggtgttccgccagggacgcgacttgtccggcttcatcgacggcaccgagaacccggccgacggaagttacgtgatcacccagcgatgggttcataaccttcccaagatcaagaagaccaaagat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sep_nuc/orthogroup_761_with_4_species.fasta Fri Feb 01 10:28:50 2019 -0500 @@ -0,0 +1,8 @@ +>Bs10197_1/1_1.000_1857 +cagatcggcttcacgaccgacccccgctcgtctcggtcgtcgccttactgcacggacgtggcgcgcgttgtcaacgcgcccatcttccacgtcaacgccgacgaccccgaggccgtgatgcacgtgtgcaaggtggctgccgagtaccgctccgagtggggcaaggacgtcgtcatcgacttggtctgttaccggcgtaatggtcacaacgagatagatgagcccatgttcacccagccgctcatgtacaagcgcatccatcagcagccatccatcctcaaactctactccgccaagctcatcgacgagaaagttgtttcgcaggatgagtatgagctcgaggtggcaaagtacgacaaaatctgcgaagacgcctatgtgaacgccaagaaggagacggtcacccgcaatagcctgtggctcgactcgccctggcccggcttcttcgacagt +>Ha1458_1/1_1.000_3087 +cagattggcttcacgacagacccccgctcatcgcgctcgtcaccctactgcacggacgtggcacgtgtcgtcaatgcacctattttccacgtaaatgccgatgaccccgaggctgtcatgcacgtatgcaaggtggcagccgagtaccgtgctgagtggggcaaagatgtggtcattgacttggtgtgctaccggaagaacggccacaatgagactgacgagcccatgttcacccaaccgctcatgtacaaacgtatccaccagcagccgtccatccttaaacagtactctacgaagctcatcaccgagggcatcgtcagccaggaagagtatgaggttgaagttgcaaagtatgacaagatttgtgaggatgcctaccttaacgcaaagaaggagacggtcacacgtaacagtcagtggctagactctccatggccaggcttctttgatcgt +>Bj16755_1/1_1.000_2085 +cagattggcttcacgactgaccctcggtcatcacggtcgtcaccgtattgcacagacgtggcacgcgtcgtgaacgcgcccatcttccacgtgaacgcggatgaccccgaagccgtcatgcatgtgtgtaaggtggctgccgagtaccgcgcagaatggggcaaggacgtcgtcattgacttggtatgctaccggcgcaatggtcacaacgagatagatgagcctatgtttacgcagccactcatgtacaagcgcatccaccagcagccgtccatccttaagctctactctgccaagctcattgatgagaaaatagtttcacaagatgaatatgaggttgaagtggcaaagtacgataaaatctgtgaagatgcttacataaatgccaagaaggagactgtcacccgcaacagtctatggctcgactcgccttggccaggattctttgactgt +>Lf14456_1/1_1.000_2623 +cagatcggcttcacgacagacccacggtcctcccgctcgtccccatactgcacggacgtggcacgtgtcgtgaacgcacctatcttccacgtgaacgcggacgaccccgaggccgtgatgcacgtgtgtaaggtggccgccgagtaccgcgccgagtggggcaaggacgtcgtcatcgacttggtgtgttatcgccgtaacggtcacaacgagatcgacgagccgatgttcacacaaccgctcatgtacaagcgtatccaccaacagccgtccatcctcaaactgtactcggcaaaactcatcgacgagaagatcgtctcacaggaggaatacgagcttgaagtggccaagtacgacaagatctgcgaggacgcgtacctgaacgccaagaaggagacagtgacccgaaacagcctatggctcgactcaccctggcccggcttcttcgatcgt