| Previous changeset 4:999060f051ac (2020-05-13) Next changeset 6:0ff17c7a18cd (2021-05-03) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder commit 8fb4e5b2821a83fda89ac616b32726714962717c" |
|
modified:
orthofinder_only_groups.xml test-data/results_fromblast/Orthogroups.txt |
|
added:
macros.xml test-data/results/Duplications.tsv test-data/results/Duplications_per_Orthogroup.tsv test-data/results/Duplications_per_Species_Tree_Node.tsv test-data/results/SpeciesTree_Gene_Duplications_0.5_Support.txt test-data/results/SpeciesTree_rooted.txt test-data/results/SpeciesTree_rooted_node_labels.txt test-data/results_fromblast/Orthogroups.tsv test-data/results_fromblast/Orthogroups_SpeciesOverlaps.tsv test-data/results_fromblast/Orthogroups_UnassignedGenes.tsv test-data/results_fromblast/Statistics_Overall.tsv test-data/results_fromblast/Statistics_PerSpecies.tsv |
|
removed:
test-data/results_fromblast/Orthogroups.csv test-data/results_fromblast/Orthogroups_SpeciesOverlaps.csv test-data/results_fromblast/Orthogroups_UnassignedGenes.csv test-data/results_fromblast/Statistics_Overall.csv test-data/results_fromblast/Statistics_PerSpecies.csv |
| b |
| diff -r 999060f051ac -r 974d8c28e586 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.4.0</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s13059-015-0721-2</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 999060f051ac -r 974d8c28e586 orthofinder_only_groups.xml --- a/orthofinder_only_groups.xml Wed May 13 01:41:06 2020 -0400 +++ b/orthofinder_only_groups.xml Mon Aug 17 12:59:19 2020 -0400 |
| [ |
| b'@@ -1,36 +1,45 @@\n-<tool name="OrthoFinder OnlyGroups" id="orthofinder_onlygroups" version="2.2.6">\n+<tool name="OrthoFinder" id="orthofinder_onlygroups" version="@TOOL_VERSION@">\n <description>finds orthogroups in a set of proteomes</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n <requirements>\n- <requirement type="package" version="2.2.6">orthofinder</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">orthofinder</requirement>\n <requirement type="package" version="2.34">util-linux</requirement>\n </requirements>\n- <command detect_errors="exit_code">\n- <![CDATA[\n+ <command detect_errors="exit_code"><![CDATA[\n+ #import re\n ## prepare inputs\n #if $init.start == "fasta":\n #set $infiles = ""\n #for $input in $init.input_fasta\n- ln -s \'$input\' \'${input.element_identifier}.fasta\' &&\n- #set $infiles = $infiles + str($input.element_identifier) + ","\n+ #set $identifier=re.sub(\'[^\\w\\-\\s\\.]\', \'_\', str($input.element_identifier))\n+ ln -s \'$input\' \'${identifier}.fasta\' &&\n+ #set $infiles = $infiles + str($identifier) + ","\n #end for\n #set $infiles = $infiles[:-1]\n #elif $init.start == "blast":\n #set $infilesbl = ""\n #for $input in $init.input_blast_out\n- ln -s \'$input\' \'$input.element_identifier\' &&\n- #set $infilesbl = $infilesbl + str($input.element_identifier) + ","\n+ #set $identifier=re.sub(\'[^\\w\\-\\s\\.]\', \'_\', str($input.element_identifier))\n+ ln -s \'$input\' \'$identifier\' &&\n+ #set $infilesbl = $infilesbl + str($identifier) + ","\n #end for\n #set $infilesbl = $infilesbl[:-1]\n \n #set $infilesfa = ""\n #for $input in $init.input_blast_fa\n- ln -s \'$input\' \'$input.element_identifier\' &&\n- #set $infilesfa = $infilesfa + str($input.element_identifier) + ","\n+ #set $identifier=re.sub(\'[^\\w\\-\\s\\.]\', \'_\', str($input.element_identifier))\n+ ln -s \'$input\' \'$identifier\' &&\n+ #set $infilesfa = $infilesfa + str($identifier) + ","\n #end for\n #set $infilesfa = $infilesfa[:-1]\n \n- ln -s $init.specIDs $init.specIDs.element_identifier &&\n- ln -s $init.seqIDs $init.seqIDs.element_identifier &&\n+ #set $identifier=re.sub(\'[^\\w\\-\\s\\.]\', \'_\', str($init.specIDs.element_identifier))\n+ ln -s $init.specIDs $identifier &&\n+\n+ #set $identifier=re.sub(\'[^\\w\\-\\s\\.]\', \'_\', str($init.seqIDs.element_identifier))\n+ ln -s $init.seqIDs $identifier &&\n #end if\n \n ## start Orthofinder\n@@ -42,10 +51,22 @@\n -b .\n #end if\n \n- -I $I -og -t \\${GALAXY_SLOTS:-1} -a \\${GALAXY_SLOTS:-1} &&\n+ -I $I\n \n+ #if $trees.run_mode == "full":\n+ -M \'${trees.tree_method.method}\'\n+ #if $trees.tree_method.method == "msa":\n+ -A \'${trees.tree_method.msa_program}\'\n+ -T \'${trees.tree_method.msa_tree_program}\'\n+ #end if\n+ #else:\n+ $trees.run_mode\n+ #end if\n+\n+ -t \\${GALAXY_SLOTS:-1} -a \\${GALAXY_SLOTS:-1} &&\n+\n+ mv OrthoFinder/Results_* results\n #if $init.start == "fasta":\n- mv Results_* results\n #if $init.search.search_program == "blast":\n #if $init.search.keepblastout:\n && mkdir -p results/WorkingDirectory/blast results/WorkingDirectory/fa &&\n@@ -53,17 +74,12 @@\n mv results/WorkingDirectory/*.fa results/WorkingDirectory/fa/\n #end if\n #end if\n- #elif $init.start == "blast":\n- mkdir results &&\n- mv *.csv results/ &&\n- mv Orthogroups.txt results/\n '..b' <has_text text="Number of genes"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- trees + diamond + input files have no extension fasta/faa/fa + msa -->\n+ <test>\n+ <conditional name="init">\n+ <param name="start" value="fasta" />\n+ <param name="input_fasta" ftype="fasta" value="inputs/proteomes/Mycoplasma_agalactiae.faa,inputs/proteomes/Mycoplasma_gallisepticum.faa,inputs/proteomes/Mycoplasma_genitalium.faa,inputs/proteomes/Mycoplasma_hyopneumoniae.faa" />\n+ <conditional name="search">\n+ <param name="search_program" value="diamond"/>\n+ </conditional>\n+ </conditional>\n+ <conditional name="trees">\n+ <param name="run_mode" value="full" />\n+ <conditional name="tree_method">\n+ <param name="method" value="msa" />\n+ <param name="msa_program" value="muscle" />\n+ <param name="msa_tree_program" value="raxml" />\n+ </conditional>\n+ </conditional>\n+ <param name="inflation" value="1.5" />\n+ <output name="specs_overlap">\n+ <assert_contents>\n+ <has_text text="Mycoplasma_agalactiae"/>\n+ <has_text text="Mycoplasma_gallisepticum"/>\n+ <has_text text="Mycoplasma_genitalium"/>\n+ <has_text text="Mycoplasma_hyopneumoniae"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="unassigned_genes">\n+ <assert_contents>\n+ <has_text text="Mycoplasma_agalactiae"/>\n+ <has_text text="Mycoplasma_gallisepticum"/>\n+ <has_text text="Mycoplasma_genitalium"/>\n+ <has_text text="Mycoplasma_hyopneumoniae"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ <output name="stat_overall">\n+ <assert_contents>\n+ <has_text text="Number of genes in orthogroups"/>\n+ <has_text text="Number of unassigned genes"/>\n+ <has_text text="Percentage of orthogroups"/>\n+ <has_text text="Number of orthogroups"/>\n+ <has_text text="Number of genes"/>\n+ <has_text text="G50 (assigned genes)"/>\n+ <has_text text="G50 (all genes)"/>\n+ <has_text text="O50 (assigned genes)"/>\n+ <has_text text="O50 (all genes)"/>\n+ </assert_contents>\n+ </output>\n+ <output name="stat_specs">\n+ <assert_contents>\n+ <has_text text="Mycoplasma_agalactiae"/>\n+ <has_text text="Mycoplasma_gallisepticum"/>\n+ <has_text text="Mycoplasma_genitalium"/>\n+ <has_text text="Mycoplasma_hyopneumoniae"/>\n+ <has_text text="Number of genes per-species in orthogroup"/>\n+ <has_text text="Percentage of orthogroups"/>\n+ <has_text text="Number of orthogroups"/>\n+ <has_text text="Number of genes"/>\n+ <has_n_columns n="5"/>\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ <has_text text="-M \'msa\'"/>\n+ <has_text text="-A \'muscle\'"/>\n+ <has_text text="-T \'raxml\'"/>\n+ </assert_command>\n </test>\n </tests>\n <help>\n@@ -429,7 +774,5 @@\n - Inflation : the inflation parameter; modify this parameter is not recommended.\n \n </help>\n- <citations>\n- <citation type="doi">10.1186/s13059-015-0721-2</citation>\n- </citations>\n+ <expand macro="citations"/>\n </tool>\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results/Duplications.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Duplications.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| b'@@ -0,0 +1,331 @@\n+Orthogroup\tSpecies Tree Node\tGene Tree Node\tSupport\tType\tGenes 1\tGenes 2\n+OG0000000\tMycoplasma_gallisepticum.faa\tn0\t1.0\tTerminal\tMycoplasma_gallisepticum_faa_gi|284812105|gb|AAP56776.2|\tMycoplasma_gallisepticum_faa_gi|284812041|gb|ADB96874.1|, Mycoplasma_gallisepticum_faa_gi|284812040|gb|ADB96873.1|, Mycoplasma_gallisepticum_faa_gi|31541396|gb|AAP56697.1|, Mycoplasma_gallisepticum_faa_gi|284812108|gb|ADB96882.1|, Mycoplasma_gallisepticum_faa_gi|31541473|gb|AAP56774.1|, Mycoplasma_gallisepticum_faa_gi|284812218|gb|ADB96892.1|, Mycoplasma_gallisepticum_faa_gi|284811957|gb|ADB96860.1|, Mycoplasma_gallisepticum_faa_gi|284811953|gb|ADB96857.1|, Mycoplasma_gallisepticum_faa_gi|31541394|gb|AAP56695.1|, Mycoplasma_gallisepticum_faa_gi|284812039|gb|AAP56686.2|, Mycoplasma_gallisepticum_faa_gi|284812129|gb|AAP56806.2|, Mycoplasma_gallisepticum_faa_gi|284812128|gb|AAP56805.2|, Mycoplasma_gallisepticum_faa_gi|31541392|gb|AAP56693.1|, Mycoplasma_gallisepticum_faa_gi|284812107|gb|ADB96881.1|, Mycoplasma_gallisepticum_faa_gi|31541248|gb|AAP56550.1|, Mycoplasma_gallisepticum_faa_gi|284811962|gb|ADB96865.1|, Mycoplasma_gallisepticum_faa_gi|31541645|gb|AAP56945.1|, Mycoplasma_gallisepticum_faa_gi|31541243|gb|AAP56545.1|, Mycoplasma_gallisepticum_faa_gi|284812217|gb|ADB96891.1|, Mycoplasma_gallisepticum_faa_gi|284812219|gb|AAP56940.2|, Mycoplasma_gallisepticum_faa_gi|31541641|gb|AAP56941.1|, Mycoplasma_gallisepticum_faa_gi|31541389|gb|AAP56690.1|, Mycoplasma_gallisepticum_faa_gi|31541472|gb|AAP56773.1|, Mycoplasma_gallisepticum_faa_gi|31541398|gb|AAP56699.1|, Mycoplasma_gallisepticum_faa_gi|31541386|gb|AAP56687.1|, Mycoplasma_gallisepticum_faa_gi|31541249|gb|AAP56551.1|, Mycoplasma_gallisepticum_faa_gi|31541644|gb|AAP56944.1|, Mycoplasma_gallisepticum_faa_gi|284811956|gb|ADB96859.1|, Mycoplasma_gallisepticum_faa_gi|31541252|gb|AAP56554.1|, Mycoplasma_gallisepticum_faa_gi|31541391|gb|AAP56692.1|, Mycoplasma_gallisepticum_faa_gi|31541395|gb|AAP56696.1|, Mycoplasma_gallisepticum_faa_gi|31541643|gb|AAP56943.1|, Mycoplasma_gallisepticum_faa_gi|31541390|gb|AAP56691.1|, Mycoplasma_gallisepticum_faa_gi|31541250|gb|AAP56552.1|, Mycoplasma_gallisepticum_faa_gi|284812103|gb|ADB96879.1|, Mycoplasma_gallisepticum_faa_gi|284812104|gb|ADB96880.1|, Mycoplasma_gallisepticum_faa_gi|31541474|gb|AAP56775.1|, Mycoplasma_gallisepticum_faa_gi|31541646|gb|AAP56946.1|, Mycoplasma_gallisepticum_faa_gi|284811958|gb|ADB96861.1|, Mycoplasma_gallisepticum_faa_gi|284811954|gb|ADB96858.1|, Mycoplasma_gallisepticum_faa_gi|31541478|gb|AAP56779.1|, Mycoplasma_gallisepticum_faa_gi|31541387|gb|AAP56688.1|, Mycoplasma_gallisepticum_faa_gi|31541642|gb|AAP56942.1|, Mycoplasma_gallisepticum_faa_gi|31541388|gb|AAP56689.1|, Mycoplasma_gallisepticum_faa_gi|31541253|gb|AAP56555.1|, Mycoplasma_gallisepticum_faa_gi|284811955|gb|AAP56548.2|, Mycoplasma_gallisepticum_faa_gi|284811960|gb|ADB96863.1|, Mycoplasma_gallisepticum_faa_gi|31541393|gb|AAP56694.1|, Mycoplasma_gallisepticum_faa_gi|284811959|gb|ADB96862.1|, Mycoplasma_gallisepticum_faa_gi|31541245|gb|AAP56547.1|, Mycoplasma_gallisepticum_faa_gi|284812042|gb|ADB96875.1|, Mycoplasma_gallisepticum_faa_gi|284811961|gb|ADB96864.1|, Mycoplasma_gallisepticum_faa_gi|31541247|gb|AAP56549.1|, Mycoplasma_gallisepticum_faa_gi|31541647|gb|AAP56947.1|\n+OG0000000\tMycoplasma_gallisepticum.faa\tn1\t1.0\tTerminal\tMycoplasma_gallisepticum_faa_gi|284812041|gb|ADB96874.1|\tMycoplasma_gallisepticum_faa_gi|284812040|gb|ADB96873.1|, Mycoplasma_gallisepticum_faa_gi|31541396|gb|AAP56697.1|, Mycoplasma_gallisepticum_faa_gi|284812108|gb|ADB96882.1|, Mycoplasma_gallisepticum_faa_gi|31541473|gb|AAP56774.1|, Mycoplasma_gallisepticum_faa_gi|284812218|gb|ADB96892.1|, Mycoplasma_gallisepticum_faa_gi|284811957|gb|ADB96860.1|, Mycoplasma_gallisepticum_faa_gi|284811953|gb|ADB96857.1|, Mycoplasma_gallisepticum_faa_gi|31541394|gb|AAP56695.1|, Mycoplasma_gallisepticum_faa_gi|284812039|gb|AAP56686.2|, Mycoplasma_gallisepticum_faa_gi|284812129|gb|AAP56806.2|, Myco'..b'lasma_agalactiae_faa_gi|290752859|emb|CBH40834.1|\tMycoplasma_agalactiae_faa_gi|290752865|emb|CBH40840.1|\n+OG0000317\tMycoplasma_gallisepticum.faa\tn1\t1.0\tTerminal\tMycoplasma_gallisepticum_faa_gi|31541321|gb|AAP56622.1|\tMycoplasma_gallisepticum_faa_gi|31541230|gb|AAP56532.1|, Mycoplasma_gallisepticum_faa_gi|284811946|gb|AAP56530.2|\n+OG0000317\tMycoplasma_gallisepticum.faa\tn2\t1.0\tTerminal\tMycoplasma_gallisepticum_faa_gi|31541230|gb|AAP56532.1|\tMycoplasma_gallisepticum_faa_gi|284811946|gb|AAP56530.2|\n+OG0000318\tMycoplasma_genitalium.faa\tn2\t1.0\tTerminal\tMycoplasma_genitalium_faa_gi|84626145|gb|AAC71447.2|\tMycoplasma_genitalium_faa_gi|3844828|gb|AAC71446.1|\n+OG0000319\tMycoplasma_genitalium.faa\tn1\t1.0\tTerminal\tMycoplasma_genitalium_faa_gi|1045743|gb|AAC71286.1|, Mycoplasma_genitalium_faa_gi|3844986|gb|AAC71623.1|\tMycoplasma_genitalium_faa_gi|1045742|gb|AAC71285.1|\n+OG0000319\tMycoplasma_genitalium.faa\tn2\t1.0\tTerminal\tMycoplasma_genitalium_faa_gi|1045743|gb|AAC71286.1|\tMycoplasma_genitalium_faa_gi|3844986|gb|AAC71623.1|\n+OG0000320\tN2\tn0\t1.0\tNon-Terminal\tMycoplasma_genitalium_faa_gi|3844975|gb|AAC71613.1|, Mycoplasma_gallisepticum_faa_gi|31541553|gb|AAP56853.1|\tMycoplasma_genitalium_faa_gi|1046012|gb|AAC71534.1|, Mycoplasma_gallisepticum_faa_gi|284812192|gb|AAP56901.2|\n+OG0000321\tMycoplasma_hyopneumoniae.faa\tn0\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|71851985|gb|AAZ44593.1|\tMycoplasma_hyopneumoniae_faa_gi|71851712|gb|AAZ44320.1|, Mycoplasma_hyopneumoniae_faa_gi|144227672|gb|AAZ44604.2|, Mycoplasma_hyopneumoniae_faa_gi|144227671|gb|AAZ44602.2|\n+OG0000321\tMycoplasma_hyopneumoniae.faa\tn1\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|71851712|gb|AAZ44320.1|\tMycoplasma_hyopneumoniae_faa_gi|144227672|gb|AAZ44604.2|, Mycoplasma_hyopneumoniae_faa_gi|144227671|gb|AAZ44602.2|\n+OG0000321\tMycoplasma_hyopneumoniae.faa\tn2\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|144227672|gb|AAZ44604.2|\tMycoplasma_hyopneumoniae_faa_gi|144227671|gb|AAZ44602.2|\n+OG0000322\tMycoplasma_hyopneumoniae.faa\tn0\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|144227676|gb|ABO93480.1|\tMycoplasma_hyopneumoniae_faa_gi|144227673|gb|AAZ44605.2|, Mycoplasma_hyopneumoniae_faa_gi|144227527|gb|AAZ44323.2|, Mycoplasma_hyopneumoniae_faa_gi|71851988|gb|AAZ44596.1|\n+OG0000322\tMycoplasma_hyopneumoniae.faa\tn1\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|144227673|gb|AAZ44605.2|, Mycoplasma_hyopneumoniae_faa_gi|144227527|gb|AAZ44323.2|\tMycoplasma_hyopneumoniae_faa_gi|71851988|gb|AAZ44596.1|\n+OG0000322\tMycoplasma_hyopneumoniae.faa\tn2\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|144227673|gb|AAZ44605.2|\tMycoplasma_hyopneumoniae_faa_gi|144227527|gb|AAZ44323.2|\n+OG0000323\tMycoplasma_hyopneumoniae.faa\tn0\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|144227586|gb|AAZ44428.2|\tMycoplasma_hyopneumoniae_faa_gi|71851817|gb|AAZ44425.1|, Mycoplasma_hyopneumoniae_faa_gi|144227585|gb|AAZ44427.2|, Mycoplasma_hyopneumoniae_faa_gi|71851803|gb|AAZ44411.1|\n+OG0000323\tMycoplasma_hyopneumoniae.faa\tn1\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|71851817|gb|AAZ44425.1|, Mycoplasma_hyopneumoniae_faa_gi|144227585|gb|AAZ44427.2|\tMycoplasma_hyopneumoniae_faa_gi|71851803|gb|AAZ44411.1|\n+OG0000323\tMycoplasma_hyopneumoniae.faa\tn2\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|71851817|gb|AAZ44425.1|\tMycoplasma_hyopneumoniae_faa_gi|144227585|gb|AAZ44427.2|\n+OG0000324\tMycoplasma_hyopneumoniae.faa\tn0\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|144227644|gb|AAZ44545.2|\tMycoplasma_hyopneumoniae_faa_gi|71851902|gb|AAZ44510.1|, Mycoplasma_hyopneumoniae_faa_gi|71851936|gb|AAZ44544.1|, Mycoplasma_hyopneumoniae_faa_gi|144227625|gb|AAZ44516.2|\n+OG0000324\tMycoplasma_hyopneumoniae.faa\tn1\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|71851902|gb|AAZ44510.1|\tMycoplasma_hyopneumoniae_faa_gi|71851936|gb|AAZ44544.1|, Mycoplasma_hyopneumoniae_faa_gi|144227625|gb|AAZ44516.2|\n+OG0000324\tMycoplasma_hyopneumoniae.faa\tn2\t1.0\tTerminal\tMycoplasma_hyopneumoniae_faa_gi|71851936|gb|AAZ44544.1|\tMycoplasma_hyopneumoniae_faa_gi|144227625|gb|AAZ44516.2|\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results/Duplications_per_Orthogroup.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Duplications_per_Orthogroup.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,326 @@ +Orthogroup Duplications (all) Duplications (50% support) +OG0000000 54 54 +OG0000001 32 32 +OG0000002 10 6 +OG0000003 14 14 +OG0000004 12 12 +OG0000005 11 11 +OG0000006 6 6 +OG0000007 3 2 +OG0000008 6 6 +OG0000009 9 9 +OG0000010 8 8 +OG0000011 7 7 +OG0000012 1 1 +OG0000013 1 1 +OG0000014 5 5 +OG0000015 4 4 +OG0000016 1 1 +OG0000017 7 7 +OG0000018 2 1 +OG0000019 6 6 +OG0000020 6 6 +OG0000021 6 6 +OG0000022 6 6 +OG0000023 3 3 +OG0000024 5 5 +OG0000025 2 2 +OG0000026 1 1 +OG0000027 1 1 +OG0000028 2 2 +OG0000029 5 5 +OG0000030 5 5 +OG0000031 1 1 +OG0000032 2 2 +OG0000033 4 4 +OG0000034 1 1 +OG0000035 1 1 +OG0000036 1 1 +OG0000037 1 1 +OG0000038 1 1 +OG0000039 2 2 +OG0000040 4 4 +OG0000041 1 1 +OG0000042 1 1 +OG0000043 1 1 +OG0000044 1 1 +OG0000045 1 1 +OG0000046 1 1 +OG0000047 1 1 +OG0000048 2 2 +OG0000049 3 3 +OG0000050 4 4 +OG0000051 4 4 +OG0000052 2 2 +OG0000053 0 0 +OG0000054 0 0 +OG0000055 0 0 +OG0000056 1 1 +OG0000057 0 0 +OG0000058 0 0 +OG0000059 0 0 +OG0000060 0 0 +OG0000061 0 0 +OG0000062 0 0 +OG0000063 0 0 +OG0000064 0 0 +OG0000065 0 0 +OG0000066 0 0 +OG0000067 0 0 +OG0000068 0 0 +OG0000069 0 0 +OG0000070 0 0 +OG0000071 0 0 +OG0000072 0 0 +OG0000073 0 0 +OG0000074 0 0 +OG0000075 0 0 +OG0000076 0 0 +OG0000077 0 0 +OG0000078 0 0 +OG0000079 0 0 +OG0000080 0 0 +OG0000081 0 0 +OG0000082 0 0 +OG0000083 0 0 +OG0000084 0 0 +OG0000085 0 0 +OG0000086 0 0 +OG0000087 0 0 +OG0000088 0 0 +OG0000089 0 0 +OG0000090 0 0 +OG0000091 0 0 +OG0000092 0 0 +OG0000093 0 0 +OG0000094 0 0 +OG0000095 0 0 +OG0000096 0 0 +OG0000097 0 0 +OG0000098 0 0 +OG0000099 0 0 +OG0000100 0 0 +OG0000101 0 0 +OG0000102 0 0 +OG0000103 0 0 +OG0000104 0 0 +OG0000105 0 0 +OG0000106 0 0 +OG0000107 0 0 +OG0000108 0 0 +OG0000109 0 0 +OG0000110 2 2 +OG0000111 0 0 +OG0000112 0 0 +OG0000113 0 0 +OG0000114 0 0 +OG0000115 1 1 +OG0000116 0 0 +OG0000117 0 0 +OG0000118 0 0 +OG0000119 0 0 +OG0000120 0 0 +OG0000121 0 0 +OG0000122 0 0 +OG0000123 0 0 +OG0000124 0 0 +OG0000125 0 0 +OG0000126 0 0 +OG0000127 0 0 +OG0000128 0 0 +OG0000129 0 0 +OG0000130 1 1 +OG0000131 1 1 +OG0000132 1 1 +OG0000133 0 0 +OG0000134 0 0 +OG0000135 0 0 +OG0000136 0 0 +OG0000137 0 0 +OG0000138 0 0 +OG0000139 0 0 +OG0000140 0 0 +OG0000141 0 0 +OG0000142 0 0 +OG0000143 0 0 +OG0000144 0 0 +OG0000145 0 0 +OG0000146 0 0 +OG0000147 0 0 +OG0000148 0 0 +OG0000149 0 0 +OG0000150 0 0 +OG0000151 2 2 +OG0000152 3 3 +OG0000153 3 3 +OG0000154 3 3 +OG0000155 2 2 +OG0000156 2 2 +OG0000157 3 3 +OG0000158 1 1 +OG0000159 0 0 +OG0000160 0 0 +OG0000161 0 0 +OG0000162 0 0 +OG0000163 1 1 +OG0000164 0 0 +OG0000165 0 0 +OG0000166 0 0 +OG0000167 0 0 +OG0000168 0 0 +OG0000169 0 0 +OG0000170 0 0 +OG0000171 0 0 +OG0000172 0 0 +OG0000173 0 0 +OG0000174 0 0 +OG0000175 0 0 +OG0000176 0 0 +OG0000177 0 0 +OG0000178 0 0 +OG0000179 0 0 +OG0000180 0 0 +OG0000181 0 0 +OG0000182 0 0 +OG0000183 0 0 +OG0000184 0 0 +OG0000185 0 0 +OG0000186 0 0 +OG0000187 0 0 +OG0000188 0 0 +OG0000189 0 0 +OG0000190 0 0 +OG0000191 0 0 +OG0000192 0 0 +OG0000193 0 0 +OG0000194 0 0 +OG0000195 0 0 +OG0000196 0 0 +OG0000197 0 0 +OG0000198 0 0 +OG0000199 0 0 +OG0000200 0 0 +OG0000201 0 0 +OG0000202 0 0 +OG0000203 0 0 +OG0000204 0 0 +OG0000205 1 1 +OG0000206 1 1 +OG0000207 0 0 +OG0000208 0 0 +OG0000209 0 0 +OG0000210 0 0 +OG0000211 0 0 +OG0000212 0 0 +OG0000213 0 0 +OG0000214 0 0 +OG0000215 0 0 +OG0000216 0 0 +OG0000217 0 0 +OG0000218 0 0 +OG0000219 0 0 +OG0000220 0 0 +OG0000221 0 0 +OG0000222 0 0 +OG0000223 0 0 +OG0000224 0 0 +OG0000225 0 0 +OG0000226 0 0 +OG0000227 0 0 +OG0000228 0 0 +OG0000229 0 0 +OG0000230 0 0 +OG0000231 0 0 +OG0000232 0 0 +OG0000233 0 0 +OG0000234 0 0 +OG0000235 0 0 +OG0000236 0 0 +OG0000237 0 0 +OG0000238 0 0 +OG0000239 0 0 +OG0000240 0 0 +OG0000241 0 0 +OG0000242 0 0 +OG0000243 0 0 +OG0000244 0 0 +OG0000245 0 0 +OG0000246 0 0 +OG0000247 0 0 +OG0000248 0 0 +OG0000249 0 0 +OG0000250 0 0 +OG0000251 0 0 +OG0000252 0 0 +OG0000253 0 0 +OG0000254 0 0 +OG0000255 0 0 +OG0000256 0 0 +OG0000257 0 0 +OG0000258 0 0 +OG0000259 0 0 +OG0000260 0 0 +OG0000261 0 0 +OG0000262 0 0 +OG0000263 0 0 +OG0000264 2 2 +OG0000265 0 0 +OG0000266 0 0 +OG0000267 0 0 +OG0000268 0 0 +OG0000269 0 0 +OG0000270 0 0 +OG0000271 0 0 +OG0000272 0 0 +OG0000273 0 0 +OG0000274 0 0 +OG0000275 0 0 +OG0000276 0 0 +OG0000277 0 0 +OG0000278 0 0 +OG0000279 0 0 +OG0000280 0 0 +OG0000281 0 0 +OG0000282 0 0 +OG0000283 0 0 +OG0000284 0 0 +OG0000285 0 0 +OG0000286 0 0 +OG0000287 0 0 +OG0000288 0 0 +OG0000289 0 0 +OG0000290 0 0 +OG0000291 0 0 +OG0000292 0 0 +OG0000293 0 0 +OG0000294 0 0 +OG0000295 0 0 +OG0000296 0 0 +OG0000297 0 0 +OG0000298 0 0 +OG0000299 0 0 +OG0000300 0 0 +OG0000301 0 0 +OG0000302 0 0 +OG0000303 0 0 +OG0000304 0 0 +OG0000305 0 0 +OG0000306 0 0 +OG0000307 0 0 +OG0000308 0 0 +OG0000309 0 0 +OG0000310 0 0 +OG0000311 0 0 +OG0000312 0 0 +OG0000313 0 0 +OG0000314 0 0 +OG0000315 0 0 +OG0000316 0 0 +OG0000317 2 2 +OG0000318 1 1 +OG0000319 2 2 +OG0000320 1 1 +OG0000321 3 3 +OG0000322 3 3 +OG0000323 3 3 +OG0000324 3 3 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results/Duplications_per_Species_Tree_Node.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/Duplications_per_Species_Tree_Node.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Species Tree Node Duplications (all) Duplications (50% support) +Mycoplasma_gallisepticum.faa 112 112 +Mycoplasma_agalactiae.faa 118 118 +N0 16 12 +N1 4 2 +Mycoplasma_genitalium.faa 7 7 +Mycoplasma_hyopneumoniae.faa 66 66 +N2 7 7 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results/SpeciesTree_Gene_Duplications_0.5_Support.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/SpeciesTree_Gene_Duplications_0.5_Support.txt Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(Mycoplasma_hyopneumoniae.faa_66:0.238439,((Mycoplasma_gallisepticum.faa_112:0.412792,Mycoplasma_genitalium.faa_7:0.455492)N2_7:0.378996,Mycoplasma_agalactiae.faa_118:0.45224)N1_2:0.238439)N0_12; \ No newline at end of file |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results/SpeciesTree_rooted.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/SpeciesTree_rooted.txt Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(Mycoplasma_hyopneumoniae.faa:0.238439,((Mycoplasma_gallisepticum.faa:0.412792,Mycoplasma_genitalium.faa:0.455492)0.947955:0.378996,Mycoplasma_agalactiae.faa:0.45224)1:0.238439); \ No newline at end of file |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results/SpeciesTree_rooted_node_labels.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results/SpeciesTree_rooted_node_labels.txt Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(Mycoplasma_hyopneumoniae.faa:0.238439,((Mycoplasma_gallisepticum.faa:0.412792,Mycoplasma_genitalium.faa:0.455492)N2:0.378996,Mycoplasma_agalactiae.faa:0.45224)N1:0.238439)N0; \ No newline at end of file |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups.csv --- a/test-data/results_fromblast/Orthogroups.csv Wed May 13 01:41:06 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,537 +0,0 @@\n-\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\r\n-OG0000000\t\tgi|284811953|gb|ADB96857.1|, gi|284811954|gb|ADB96858.1|, gi|284811955|gb|AAP56548.2|, gi|284811956|gb|ADB96859.1|, gi|284811957|gb|ADB96860.1|, gi|284811958|gb|ADB96861.1|, gi|284811959|gb|ADB96862.1|, gi|284811960|gb|ADB96863.1|, gi|284811961|gb|ADB96864.1|, gi|284811962|gb|ADB96865.1|, gi|284812039|gb|AAP56686.2|, gi|284812040|gb|ADB96873.1|, gi|284812041|gb|ADB96874.1|, gi|284812042|gb|ADB96875.1|, gi|284812103|gb|ADB96879.1|, gi|284812104|gb|ADB96880.1|, gi|284812105|gb|AAP56776.2|, gi|284812107|gb|ADB96881.1|, gi|284812108|gb|ADB96882.1|, gi|284812128|gb|AAP56805.2|, gi|284812129|gb|AAP56806.2|, gi|284812217|gb|ADB96891.1|, gi|284812218|gb|ADB96892.1|, gi|284812219|gb|AAP56940.2|, gi|31541243|gb|AAP56545.1|, gi|31541245|gb|AAP56547.1|, gi|31541247|gb|AAP56549.1|, gi|31541248|gb|AAP56550.1|, gi|31541249|gb|AAP56551.1|, gi|31541250|gb|AAP56552.1|, gi|31541251|gb|AAP56553.1|, gi|31541252|gb|AAP56554.1|, gi|31541253|gb|AAP56555.1|, gi|31541386|gb|AAP56687.1|, gi|31541387|gb|AAP56688.1|, gi|31541388|gb|AAP56689.1|, gi|31541389|gb|AAP56690.1|, gi|31541390|gb|AAP56691.1|, gi|31541391|gb|AAP56692.1|, gi|31541392|gb|AAP56693.1|, gi|31541393|gb|AAP56694.1|, gi|31541394|gb|AAP56695.1|, gi|31541395|gb|AAP56696.1|, gi|31541396|gb|AAP56697.1|, gi|31541398|gb|AAP56699.1|, gi|31541472|gb|AAP56773.1|, gi|31541473|gb|AAP56774.1|, gi|31541474|gb|AAP56775.1|, gi|31541478|gb|AAP56779.1|, gi|31541641|gb|AAP56941.1|, gi|31541642|gb|AAP56942.1|, gi|31541643|gb|AAP56943.1|, gi|31541644|gb|AAP56944.1|, gi|31541645|gb|AAP56945.1|, gi|31541646|gb|AAP56946.1|, gi|31541647|gb|AAP56947.1|\t\t\r\n-OG0000001\tgi|290752501|emb|CBH40473.1|, gi|290752503|emb|CBH40475.1|, gi|290752692|emb|CBH40666.1|, gi|290752693|emb|CBH40667.1|, gi|290752812|emb|CBH40787.1|, gi|290752813|emb|CBH40788.1|, gi|290752814|emb|CBH40789.1|, gi|290752815|emb|CBH40790.1|, gi|290752816|emb|CBH40791.1|, gi|290752817|emb|CBH40792.1|, gi|290752818|emb|CBH40793.1|, gi|290753029|emb|CBH41005.1|, gi|290753030|emb|CBH41006.1|, gi|290753031|emb|CBH41007.1|, gi|290753032|emb|CBH41008.1|, gi|290753033|emb|CBH41009.1|, gi|290753034|emb|CBH41010.1|, gi|290753035|emb|CBH41011.1|, gi|290753036|emb|CBH41012.1|, gi|290753037|emb|CBH41013.1|, gi|290753040|emb|CBH41016.1|, gi|290753041|emb|CBH41017.1|, gi|290753042|emb|CBH41018.1|, gi|290753043|emb|CBH41019.1|, gi|290753044|emb|CBH41020.1|, gi|290753045|emb|CBH41021.1|, gi|290753046|emb|CBH41022.1|\t\t\t\r\n-OG0000002\tgi|290752526|emb|CBH40498.1|, gi|290752801|emb|CBH40776.1|, gi|290752802|emb|CBH40777.1|, gi|290753081|emb|CBH41057.1|\tgi|31541070|gb|AAP56372.1|, gi|31541268|gb|AAP56569.1|, gi|31541628|gb|AAP56928.1|, gi|31541629|gb|AAP56929.1|\tgi|1045740|gb|AAC71283.1|, gi|1045987|gb|AAC71511.1|, gi|3844775|gb|AAC71398.1|, gi|3844776|gb|AAC71399.1|, gi|3844882|gb|AAC71525.1|, gi|3845062|gb|AAC72487.1|, gi|3845064|gb|AAC72489.1|, gi|84626133|gb|AAC71526.2|\tgi|144227640|gb|AAZ44535.2|, gi|71851738|gb|AAZ44346.1|, gi|71851739|gb|AAZ44347.1|, gi|71851837|gb|AAZ44445.1|\r\n-OG0000003\tgi|290752269|emb|CBH40240.1|, gi|290752270|emb|CBH40241.1|, gi|290752414|emb|CBH40385.1|, gi|290752490|emb|CBH40462.1|, gi|290752766|emb|CBH40741.1|\tgi|31541260|gb|AAP56562.1|, gi|31541382|gb|AAP56683.1|\tgi|1046010|gb|AAC71532.1|, gi|3844907|gb|AAC71551.1|, gi|3844927|gb|AAC71569.1|\tgi|144227478|gb|AAZ44221.2|\r\n-OG0000004\tgi|290753066|emb|CBH41042.1|\tgi|284811924|gb|AAP56500.2|, gi|284811927|gb|ADB96855.1|, gi|284811928|gb|ADB96856.1|, gi|284812192|gb|AAP56901.2|, gi|31541553|gb|AAP56853.1|\tgi|1046012|gb|AAC71534.1|, gi|3844628|gb|AAC71235.1|, gi|3844797|gb|AAC71418.1|, gi|3844975|gb|AAC71613.1|\tgi|71851550|gb|AAZ44158.1|\r\n-OG0000005\tgi|290752591|emb|CBH40563.1|, gi|290752592|emb|CBH40564.1|, gi|290752893|emb|CBH40868.1|, gi|290752894|emb|CBH40869.1|\tgi|284811835|gb|AAP56356.2|, gi|284812058|gb|AAP56715.2|, gi|31541415|gb|AAP56716.1|\tgi|1045683|gb|AAC71230.1|, '..b'477\t\tgi|284811945|gb|AAP56529.2|\tgi|3844895|gb|AAC71540.1|\t\r\n-OG0000478\t\tgi|284811949|gb|AAP56536.2|\tgi|1045973|gb|AAC71500.1|\t\r\n-OG0000479\t\tgi|284811950|gb|AAP56538.2|\tgi|1045972|gb|AAC71499.1|\t\r\n-OG0000480\t\tgi|31541239|gb|AAP56541.1|\tgi|3844896|gb|AAC71541.1|\t\r\n-OG0000481\t\tgi|284811951|gb|AAP56544.2|\t\tgi|144227642|gb|AAZ44540.2|\r\n-OG0000482\t\tgi|284811972|gb|AAP56572.2|\tgi|1045980|gb|AAC71506.1|\t\r\n-OG0000483\t\tgi|31541272|gb|AAP56573.1|\tgi|1045981|gb|AAC71507.1|\t\r\n-OG0000484\t\tgi|284811973|gb|AAP56574.2|\tgi|1045982|gb|AAC71508.1|\t\r\n-OG0000485\t\tgi|284811978|gb|AAP56579.2|\tgi|3845040|gb|AAC72467.1|\t\r\n-OG0000486\t\tgi|31541293|gb|AAP56594.1|\tgi|1045977|gb|AAC71503.1|\t\r\n-OG0000487\t\tgi|284811990|gb|AAP56599.2|\t\tgi|144227563|gb|AAZ44390.2|\r\n-OG0000488\t\tgi|284811995|gb|AAP56607.2|\t\tgi|144227427|gb|AAZ44116.2|\r\n-OG0000489\t\tgi|284812002|gb|AAP56617.2|\tgi|3844925|gb|AAC71567.1|\t\r\n-OG0000490\t\tgi|284812013|gb|AAP56637.2|\tgi|3845048|gb|AAC72474.1|\t\r\n-OG0000491\t\tgi|31541356|gb|AAP56657.1|\tgi|3844990|gb|AAC71626.1|\t\r\n-OG0000492\t\tgi|31541362|gb|AAP56663.1|\t\tgi|71851833|gb|AAZ44441.1|\r\n-OG0000493\t\tgi|284812025|gb|AAP56664.2|\tgi|3844809|gb|AAC71429.1|\t\r\n-OG0000494\t\tgi|31541364|gb|AAP56665.1|\tgi|84626132|gb|ABC59631.1|\t\r\n-OG0000495\t\tgi|31541370|gb|AAP56671.1|\tgi|3844818|gb|AAC71437.1|\t\r\n-OG0000496\t\tgi|31541380|gb|AAP56681.1|\tgi|1045963|gb|AAC71491.1|\t\r\n-OG0000497\t\tgi|284812060|gb|AAP56718.2|\tgi|3844837|gb|AAC71454.1|\t\r\n-OG0000498\t\tgi|284812061|gb|AAP56721.2|\tgi|3844840|gb|AAC71457.1|\t\r\n-OG0000499\t\tgi|284812062|gb|AAP56722.2|\tgi|3844841|gb|AAC71458.1|\t\r\n-OG0000500\t\tgi|284812074|gb|AAP56734.2|\tgi|3844846|gb|AAC71463.1|\t\r\n-OG0000501\t\tgi|284812077|gb|AAP56738.2|\tgi|1045939|gb|AAC71468.1|\t\r\n-OG0000502\t\tgi|31541448|gb|AAP56749.1|\tgi|3844826|gb|AAC71444.1|\t\r\n-OG0000503\t\tgi|284812091|gb|AAP56756.2|\tgi|3844811|gb|AAC71430.1|\t\r\n-OG0000504\t\tgi|31541465|gb|AAP56766.1|\t\tgi|144227651|gb|AAZ44558.2|\r\n-OG0000505\t\tgi|31541498|gb|AAP56798.1|\tgi|3844971|gb|AAC71609.1|\t\r\n-OG0000506\t\tgi|284812125|gb|AAP56801.2|\tgi|3844978|gb|AAC71616.1|\t\r\n-OG0000507\t\tgi|31541512|gb|AAP56812.1|\tgi|3844689|gb|AAC71319.1|\t\r\n-OG0000508\t\tgi|284812140|gb|AAP56821.2|\tgi|3844721|gb|AAC71348.1|\t\r\n-OG0000509\t\tgi|284812145|gb|AAP56827.2|\tgi|84626131|gb|AAC71620.2|\t\r\n-OG0000510\t\tgi|31541528|gb|AAP56828.1|\tgi|3844984|gb|AAC71621.1|\t\r\n-OG0000511\t\tgi|31541549|gb|AAP56849.1|\tgi|3844959|gb|AAC71598.1|\t\r\n-OG0000512\t\tgi|31541558|gb|AAP56858.1|\tgi|3844638|gb|AAC71244.1|\t\r\n-OG0000513\t\tgi|284812164|gb|AAP56866.2|\tgi|3844898|gb|AAC71543.1|\t\r\n-OG0000514\t\tgi|284812171|gb|AAP56875.2|\tgi|84626128|gb|AAC71502.2|\t\r\n-OG0000515\t\tgi|284812173|gb|AAP56879.2|\tgi|3845020|gb|AAC72448.1|\t\r\n-OG0000516\t\tgi|31541590|gb|AAP56890.1|\tgi|3844885|gb|AAC71528.1|\t\r\n-OG0000517\t\tgi|31541595|gb|AAP56895.1|\tgi|3844719|gb|AAC71346.1|\t\r\n-OG0000518\t\tgi|284812188|gb|AAP56896.2|\tgi|3844718|gb|AAC71345.1|\t\r\n-OG0000519\t\tgi|284812202|gb|AAP56917.2|\tgi|3844893|gb|AAC71538.1|\t\r\n-OG0000520\t\tgi|284812208|gb|AAP56924.2|\tgi|1045731|gb|AAC71274.1|\t\r\n-OG0000521\t\tgi|284812210|gb|AAP56926.2|\tgi|3844778|gb|AAC71401.1|\t\r\n-OG0000522\t\tgi|31541648|gb|AAP56948.1|\tgi|1045712|gb|AAC71256.1|\t\r\n-OG0000523\t\tgi|31541655|gb|AAP56955.1|\tgi|3844989|gb|AAC71625.1|\t\r\n-OG0000524\t\tgi|284812225|gb|AAP56960.2|\tgi|3844682|gb|AAC71313.1|\t\r\n-OG0000525\t\tgi|284812227|gb|AAP56967.2|\tgi|3844647|gb|AAC71253.1|\t\r\n-OG0000526\t\tgi|284812245|gb|AAP56998.2|\tgi|1045728|gb|AAC71271.1|\t\r\n-OG0000527\t\tgi|284812254|gb|AAP57010.2|\tgi|3844631|gb|AAC71238.1|\t\r\n-OG0000528\t\tgi|31541720|gb|AAP57020.1|\t\tgi|144227662|gb|AAZ44577.2|\r\n-OG0000529\t\tgi|284812281|gb|AAP57051.2|\tgi|3845001|gb|AAC71636.1|\t\r\n-OG0000530\t\tgi|284812282|gb|AAP57052.2|\tgi|84626126|gb|AAC71234.2|\t\r\n-OG0000531\t\tgi|31541763|gb|AAP57062.1|\tgi|84626158|gb|AAC72481.2|\t\r\n-OG0000532\t\tgi|284812300|gb|AAP57075.2|\tgi|84626152|gb|AAC71218.2|\t\r\n-OG0000533\t\t\tgi|84626147|gb|AAC71280.2|\tgi|71851703|gb|AAZ44311.1|\r\n-OG0000534\t\t\tgi|3844705|gb|AAC71333.1|\tgi|71851627|gb|AAZ44235.1|\r\n-OG0000535\t\t\tgi|3844873|gb|AAC71515.1|\tgi|71851777|gb|AAZ44385.1|\r\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| b'@@ -0,0 +1,623 @@\n+Orthogroup\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\n+OG0000000\t\tgi|284811952|gb|AAP56546.2|, gi|284811953|gb|ADB96857.1|, gi|284811954|gb|ADB96858.1|, gi|284811955|gb|AAP56548.2|, gi|284811956|gb|ADB96859.1|, gi|284811957|gb|ADB96860.1|, gi|284811958|gb|ADB96861.1|, gi|284811959|gb|ADB96862.1|, gi|284811960|gb|ADB96863.1|, gi|284811961|gb|ADB96864.1|, gi|284811962|gb|ADB96865.1|, gi|284812039|gb|AAP56686.2|, gi|284812040|gb|ADB96873.1|, gi|284812041|gb|ADB96874.1|, gi|284812042|gb|ADB96875.1|, gi|284812103|gb|ADB96879.1|, gi|284812104|gb|ADB96880.1|, gi|284812105|gb|AAP56776.2|, gi|284812107|gb|ADB96881.1|, gi|284812108|gb|ADB96882.1|, gi|284812128|gb|AAP56805.2|, gi|284812129|gb|AAP56806.2|, gi|284812217|gb|ADB96891.1|, gi|284812218|gb|ADB96892.1|, gi|284812219|gb|AAP56940.2|, gi|31541243|gb|AAP56545.1|, gi|31541245|gb|AAP56547.1|, gi|31541247|gb|AAP56549.1|, gi|31541248|gb|AAP56550.1|, gi|31541249|gb|AAP56551.1|, gi|31541250|gb|AAP56552.1|, gi|31541251|gb|AAP56553.1|, gi|31541252|gb|AAP56554.1|, gi|31541253|gb|AAP56555.1|, gi|31541386|gb|AAP56687.1|, gi|31541387|gb|AAP56688.1|, gi|31541388|gb|AAP56689.1|, gi|31541389|gb|AAP56690.1|, gi|31541390|gb|AAP56691.1|, gi|31541391|gb|AAP56692.1|, gi|31541392|gb|AAP56693.1|, gi|31541393|gb|AAP56694.1|, gi|31541394|gb|AAP56695.1|, gi|31541395|gb|AAP56696.1|, gi|31541396|gb|AAP56697.1|, gi|31541398|gb|AAP56699.1|, gi|31541472|gb|AAP56773.1|, gi|31541473|gb|AAP56774.1|, gi|31541474|gb|AAP56775.1|, gi|31541477|gb|AAP56778.1|, gi|31541478|gb|AAP56779.1|, gi|31541641|gb|AAP56941.1|, gi|31541642|gb|AAP56942.1|, gi|31541643|gb|AAP56943.1|, gi|31541644|gb|AAP56944.1|, gi|31541645|gb|AAP56945.1|, gi|31541646|gb|AAP56946.1|, gi|31541647|gb|AAP56947.1|\t\t\n+OG0000001\tgi|290752409|emb|CBH40380.1|, gi|290752502|emb|CBH40474.1|, gi|290752505|emb|CBH40477.1|, gi|290752512|emb|CBH40484.1|, gi|290752622|emb|CBH40595.1|, gi|290752623|emb|CBH40596.1|, gi|290752688|emb|CBH40662.1|, gi|290752690|emb|CBH40664.1|, gi|290752693|emb|CBH40667.1|, gi|290752812|emb|CBH40787.1|, gi|290752813|emb|CBH40788.1|, gi|290752814|emb|CBH40789.1|, gi|290752815|emb|CBH40790.1|, gi|290752816|emb|CBH40791.1|, gi|290752817|emb|CBH40792.1|, gi|290752818|emb|CBH40793.1|, gi|290752903|emb|CBH40878.1|, gi|290752914|emb|CBH40889.1|, gi|290752941|emb|CBH40916.1|, gi|290752966|emb|CBH40941.1|, gi|290752972|emb|CBH40947.1|, gi|290753029|emb|CBH41005.1|, gi|290753030|emb|CBH41006.1|, gi|290753031|emb|CBH41007.1|, gi|290753032|emb|CBH41008.1|, gi|290753033|emb|CBH41009.1|, gi|290753034|emb|CBH41010.1|, gi|290753035|emb|CBH41011.1|, gi|290753036|emb|CBH41012.1|, gi|290753037|emb|CBH41013.1|, gi|290753040|emb|CBH41016.1|, gi|290753041|emb|CBH41017.1|, gi|290753042|emb|CBH41018.1|, gi|290753043|emb|CBH41019.1|, gi|290753044|emb|CBH41020.1|, gi|290753045|emb|CBH41021.1|, gi|290753046|emb|CBH41022.1|, gi|290753052|emb|CBH41028.1|, gi|290753065|emb|CBH41041.1|\t\t\t\n+OG0000002\tgi|290752526|emb|CBH40498.1|, gi|290752592|emb|CBH40564.1|, gi|290752801|emb|CBH40776.1|, gi|290752802|emb|CBH40777.1|, gi|290752894|emb|CBH40869.1|, gi|290753081|emb|CBH41057.1|\tgi|284811859|gb|AAP56391.2|, gi|284812058|gb|AAP56715.2|, gi|31541070|gb|AAP56372.1|, gi|31541268|gb|AAP56569.1|, gi|31541628|gb|AAP56928.1|, gi|31541629|gb|AAP56929.1|\tgi|1045683|gb|AAC71230.1|, gi|1045740|gb|AAC71283.1|, gi|1045987|gb|AAC71511.1|, gi|3844775|gb|AAC71398.1|, gi|3844776|gb|AAC71399.1|, gi|3844882|gb|AAC71525.1|, gi|3845003|gb|AAC71638.1|, gi|3845062|gb|AAC72487.1|, gi|3845064|gb|AAC72489.1|, gi|84626133|gb|AAC71526.2|\tgi|144227640|gb|AAZ44535.2|, gi|71851738|gb|AAZ44346.1|, gi|71851739|gb|AAZ44347.1|, gi|71851837|gb|AAZ44445.1|\n+OG0000003\tgi|290752288|emb|CBH40259.1|, gi|290752368|emb|CBH40339.1|, gi|290752419|emb|CBH40390.1|, gi|290752473|emb|CBH40445.1|, gi|290752611|emb|CBH40583.1|, gi|290752636|emb|CBH40609.1|, gi|290752643|emb|CBH40616.1|, gi|290752719|emb|CBH40693.1|, gi|290752768|emb|CBH40743.1|, gi|29075'..b'563\t\tgi|284812060|gb|AAP56718.2|\tgi|3844837|gb|AAC71454.1|\t\n+OG0000564\t\tgi|284812061|gb|AAP56721.2|\tgi|3844840|gb|AAC71457.1|\t\n+OG0000565\t\tgi|284812062|gb|AAP56722.2|\tgi|3844841|gb|AAC71458.1|\t\n+OG0000566\t\tgi|284812077|gb|AAP56738.2|\tgi|1045939|gb|AAC71468.1|\t\n+OG0000567\t\tgi|31541448|gb|AAP56749.1|\tgi|3844826|gb|AAC71444.1|\t\n+OG0000568\t\tgi|284812091|gb|AAP56756.2|\tgi|3844811|gb|AAC71430.1|\t\n+OG0000569\t\tgi|31541465|gb|AAP56766.1|\t\tgi|144227651|gb|AAZ44558.2|\n+OG0000570\t\tgi|284812117|gb|AAP56791.2|, gi|284812118|gb|AAP56792.2|\t\t\n+OG0000571\t\tgi|31541498|gb|AAP56798.1|\tgi|3844971|gb|AAC71609.1|\t\n+OG0000572\t\tgi|284812125|gb|AAP56801.2|\tgi|3844978|gb|AAC71616.1|\t\n+OG0000573\t\tgi|31541512|gb|AAP56812.1|\tgi|3844689|gb|AAC71319.1|\t\n+OG0000574\t\tgi|284812140|gb|AAP56821.2|\tgi|3844721|gb|AAC71348.1|\t\n+OG0000575\t\tgi|284812145|gb|AAP56827.2|\tgi|84626131|gb|AAC71620.2|\t\n+OG0000576\t\tgi|31541528|gb|AAP56828.1|\tgi|3844984|gb|AAC71621.1|\t\n+OG0000577\t\tgi|31541549|gb|AAP56849.1|\tgi|3844959|gb|AAC71598.1|\t\n+OG0000578\t\tgi|31541558|gb|AAP56858.1|\tgi|3844638|gb|AAC71244.1|\t\n+OG0000579\t\tgi|284812164|gb|AAP56866.2|\tgi|3844898|gb|AAC71543.1|\t\n+OG0000580\t\tgi|284812171|gb|AAP56875.2|\tgi|84626128|gb|AAC71502.2|\t\n+OG0000581\t\tgi|284812173|gb|AAP56879.2|\tgi|3845020|gb|AAC72448.1|\t\n+OG0000582\t\tgi|31541590|gb|AAP56890.1|\tgi|3844885|gb|AAC71528.1|\t\n+OG0000583\t\tgi|31541595|gb|AAP56895.1|\tgi|3844719|gb|AAC71346.1|\t\n+OG0000584\t\tgi|284812188|gb|AAP56896.2|\tgi|3844718|gb|AAC71345.1|\t\n+OG0000585\t\tgi|284812202|gb|AAP56917.2|\tgi|3844893|gb|AAC71538.1|\t\n+OG0000586\t\tgi|284812208|gb|AAP56924.2|\tgi|1045731|gb|AAC71274.1|\t\n+OG0000587\t\tgi|284812210|gb|AAP56926.2|\tgi|3844778|gb|AAC71401.1|\t\n+OG0000588\t\tgi|31541648|gb|AAP56948.1|\tgi|1045712|gb|AAC71256.1|\t\n+OG0000589\t\tgi|31541655|gb|AAP56955.1|\tgi|3844989|gb|AAC71625.1|\t\n+OG0000590\t\tgi|284812225|gb|AAP56960.2|\tgi|3844682|gb|AAC71313.1|\t\n+OG0000591\t\tgi|284812227|gb|AAP56967.2|\tgi|3844647|gb|AAC71253.1|\t\n+OG0000592\t\tgi|284812245|gb|AAP56998.2|\tgi|1045728|gb|AAC71271.1|\t\n+OG0000593\t\tgi|284812254|gb|AAP57010.2|\tgi|3844631|gb|AAC71238.1|\t\n+OG0000594\t\tgi|31541720|gb|AAP57020.1|\t\tgi|144227662|gb|AAZ44577.2|\n+OG0000595\t\tgi|284812269|gb|AAP57033.2|, gi|284812270|gb|AAP57034.2|\t\t\n+OG0000596\t\tgi|284812273|gb|AAP57041.2|, gi|31541743|gb|AAP57042.1|\t\t\n+OG0000597\t\tgi|284812281|gb|AAP57051.2|\tgi|3845001|gb|AAC71636.1|\t\n+OG0000598\t\tgi|284812282|gb|AAP57052.2|\tgi|84626126|gb|AAC71234.2|\t\n+OG0000599\t\tgi|31541763|gb|AAP57062.1|\tgi|84626158|gb|AAC72481.2|\t\n+OG0000600\t\tgi|284812300|gb|AAP57075.2|\tgi|84626152|gb|AAC71218.2|\t\n+OG0000601\t\t\tgi|3844623|gb|AAC71227.1|, gi|3844624|gb|AAC71228.1|\t\n+OG0000602\t\t\tgi|1045703|gb|AAC71248.1|, gi|3844684|gb|AAC71314.1|\t\n+OG0000603\t\t\tgi|84626147|gb|AAC71280.2|\tgi|71851703|gb|AAZ44311.1|\n+OG0000604\t\t\tgi|3844705|gb|AAC71333.1|\tgi|71851627|gb|AAZ44235.1|\n+OG0000605\t\t\tgi|3844873|gb|AAC71515.1|\tgi|71851777|gb|AAZ44385.1|\n+OG0000606\t\t\tgi|3845032|gb|AAC72459.1|, gi|3845033|gb|AAC72460.1|\t\n+OG0000607\t\t\t\tgi|144227458|gb|AAZ44178.2|, gi|144227569|gb|AAZ44403.2|\n+OG0000608\t\t\t\tgi|144227460|gb|AAZ44180.2|, gi|144227571|gb|AAZ44405.2|\n+OG0000609\t\t\t\tgi|144227521|gb|AAZ44313.2|, gi|71851711|gb|AAZ44319.1|\n+OG0000610\t\t\t\tgi|144227523|gb|AAZ44316.2|, gi|144227668|gb|AAZ44598.2|\n+OG0000611\t\t\t\tgi|144227524|gb|AAZ44317.2|, gi|71851991|gb|AAZ44599.1|\n+OG0000612\t\t\t\tgi|144227525|gb|AAZ44321.2|, gi|71851986|gb|AAZ44594.1|\n+OG0000613\t\t\t\tgi|144227526|gb|AAZ44322.2|, gi|144227667|gb|AAZ44595.2|\n+OG0000614\t\t\t\tgi|144227553|gb|AAZ44372.2|, gi|144227582|gb|AAZ44423.2|\n+OG0000615\t\t\t\tgi|144227575|gb|AAZ44409.2|, gi|71851802|gb|AAZ44410.1|\n+OG0000616\t\t\t\tgi|144227579|gb|AAZ44419.2|, gi|144227580|gb|AAZ44420.2|\n+OG0000617\t\t\t\tgi|71851864|gb|AAZ44472.1|, gi|71851869|gb|AAZ44477.1|\n+OG0000618\t\t\t\tgi|71851867|gb|AAZ44475.1|, gi|71851872|gb|AAZ44480.1|\n+OG0000619\t\t\t\tgi|71852040|gb|AAZ44648.1|, gi|71852043|gb|AAZ44651.1|\n+OG0000620\t\t\t\tgi|144227700|gb|AAZ44653.2|, gi|71852048|gb|AAZ44656.1|\n+OG0000621\t\t\t\tgi|144227732|gb|AAZ44712.2|, gi|71852101|gb|AAZ44709.1|\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups.txt --- a/test-data/results_fromblast/Orthogroups.txt Wed May 13 01:41:06 2020 -0400 +++ b/test-data/results_fromblast/Orthogroups.txt Mon Aug 17 12:59:19 2020 -0400 |
| b |
| b'@@ -1,1331 +1,1079 @@\n-OG0000000: gi|284811953|gb|ADB96857.1| gi|284811954|gb|ADB96858.1| gi|284811955|gb|AAP56548.2| gi|284811956|gb|ADB96859.1| gi|284811957|gb|ADB96860.1| gi|284811958|gb|ADB96861.1| gi|284811959|gb|ADB96862.1| gi|284811960|gb|ADB96863.1| gi|284811961|gb|ADB96864.1| gi|284811962|gb|ADB96865.1| gi|284812039|gb|AAP56686.2| gi|284812040|gb|ADB96873.1| gi|284812041|gb|ADB96874.1| gi|284812042|gb|ADB96875.1| gi|284812103|gb|ADB96879.1| gi|284812104|gb|ADB96880.1| gi|284812105|gb|AAP56776.2| gi|284812107|gb|ADB96881.1| gi|284812108|gb|ADB96882.1| gi|284812128|gb|AAP56805.2| gi|284812129|gb|AAP56806.2| gi|284812217|gb|ADB96891.1| gi|284812218|gb|ADB96892.1| gi|284812219|gb|AAP56940.2| gi|31541243|gb|AAP56545.1| gi|31541245|gb|AAP56547.1| gi|31541247|gb|AAP56549.1| gi|31541248|gb|AAP56550.1| gi|31541249|gb|AAP56551.1| gi|31541250|gb|AAP56552.1| gi|31541251|gb|AAP56553.1| gi|31541252|gb|AAP56554.1| gi|31541253|gb|AAP56555.1| gi|31541386|gb|AAP56687.1| gi|31541387|gb|AAP56688.1| gi|31541388|gb|AAP56689.1| gi|31541389|gb|AAP56690.1| gi|31541390|gb|AAP56691.1| gi|31541391|gb|AAP56692.1| gi|31541392|gb|AAP56693.1| gi|31541393|gb|AAP56694.1| gi|31541394|gb|AAP56695.1| gi|31541395|gb|AAP56696.1| gi|31541396|gb|AAP56697.1| gi|31541398|gb|AAP56699.1| gi|31541472|gb|AAP56773.1| gi|31541473|gb|AAP56774.1| gi|31541474|gb|AAP56775.1| gi|31541478|gb|AAP56779.1| gi|31541641|gb|AAP56941.1| gi|31541642|gb|AAP56942.1| gi|31541643|gb|AAP56943.1| gi|31541644|gb|AAP56944.1| gi|31541645|gb|AAP56945.1| gi|31541646|gb|AAP56946.1| gi|31541647|gb|AAP56947.1|\n-OG0000001: gi|290752501|emb|CBH40473.1| gi|290752503|emb|CBH40475.1| gi|290752692|emb|CBH40666.1| gi|290752693|emb|CBH40667.1| gi|290752812|emb|CBH40787.1| gi|290752813|emb|CBH40788.1| gi|290752814|emb|CBH40789.1| gi|290752815|emb|CBH40790.1| gi|290752816|emb|CBH40791.1| gi|290752817|emb|CBH40792.1| gi|290752818|emb|CBH40793.1| gi|290753029|emb|CBH41005.1| gi|290753030|emb|CBH41006.1| gi|290753031|emb|CBH41007.1| gi|290753032|emb|CBH41008.1| gi|290753033|emb|CBH41009.1| gi|290753034|emb|CBH41010.1| gi|290753035|emb|CBH41011.1| gi|290753036|emb|CBH41012.1| gi|290753037|emb|CBH41013.1| gi|290753040|emb|CBH41016.1| gi|290753041|emb|CBH41017.1| gi|290753042|emb|CBH41018.1| gi|290753043|emb|CBH41019.1| gi|290753044|emb|CBH41020.1| gi|290753045|emb|CBH41021.1| gi|290753046|emb|CBH41022.1|\n-OG0000002: gi|1045740|gb|AAC71283.1| gi|1045987|gb|AAC71511.1| gi|144227640|gb|AAZ44535.2| gi|290752526|emb|CBH40498.1| gi|290752801|emb|CBH40776.1| gi|290752802|emb|CBH40777.1| gi|290753081|emb|CBH41057.1| gi|31541070|gb|AAP56372.1| gi|31541268|gb|AAP56569.1| gi|31541628|gb|AAP56928.1| gi|31541629|gb|AAP56929.1| gi|3844775|gb|AAC71398.1| gi|3844776|gb|AAC71399.1| gi|3844882|gb|AAC71525.1| gi|3845062|gb|AAC72487.1| gi|3845064|gb|AAC72489.1| gi|71851738|gb|AAZ44346.1| gi|71851739|gb|AAZ44347.1| gi|71851837|gb|AAZ44445.1| gi|84626133|gb|AAC71526.2|\n-OG0000003: gi|1046010|gb|AAC71532.1| gi|144227478|gb|AAZ44221.2| gi|290752269|emb|CBH40240.1| gi|290752270|emb|CBH40241.1| gi|290752414|emb|CBH40385.1| gi|290752490|emb|CBH40462.1| gi|290752766|emb|CBH40741.1| gi|31541260|gb|AAP56562.1| gi|31541382|gb|AAP56683.1| gi|3844907|gb|AAC71551.1| gi|3844927|gb|AAC71569.1|\n-OG0000004: gi|1046012|gb|AAC71534.1| gi|284811924|gb|AAP56500.2| gi|284811927|gb|ADB96855.1| gi|284811928|gb|ADB96856.1| gi|284812192|gb|AAP56901.2| gi|290753066|emb|CBH41042.1| gi|31541553|gb|AAP56853.1| gi|3844628|gb|AAC71235.1| gi|3844797|gb|AAC71418.1| gi|3844975|gb|AAC71613.1| gi|71851550|gb|AAZ44158.1|\n-OG0000005: gi|1045683|gb|AAC71230.1| gi|1045684|gb|AAC71231.1| gi|284811835|gb|AAP56356.2| gi|284812058|gb|AAP56715.2| gi|290752591|emb|CBH40563.1| gi|290752592|emb|CBH40564.1| gi|290752893|emb|CBH40868.1| gi|290752894|emb|CBH40869.1| gi|31541415|gb|AAP56716.1|\n-OG0000006: gi|31541304|gb|AAP56605.1| gi|71851504|gb|AAZ44112.1| gi|71851505|gb|AAZ44113.1| gi|71851506|gb|AAZ44114.1| gi|71851779|gb|AAZ44387.1| gi|71851788|gb|AAZ44396.1| gi|71851789|gb|'..b'8: gi|144227455|gb|AAZ44175.2|\n+OG0000979: gi|144227456|gb|ABO93470.1|\n+OG0000980: gi|144227457|gb|ABO93471.1|\n+OG0000981: gi|144227464|gb|AAZ44184.2|\n+OG0000982: gi|144227470|gb|ABO93472.1|\n+OG0000983: gi|71851587|gb|AAZ44195.1|\n+OG0000984: gi|71851592|gb|AAZ44200.1|\n+OG0000985: gi|144227472|gb|AAZ44207.2|\n+OG0000986: gi|71851608|gb|AAZ44216.1|\n+OG0000987: gi|144227481|gb|AAZ44225.2|\n+OG0000988: gi|144227484|gb|AAZ44229.2|\n+OG0000989: gi|144227489|gb|AAZ44237.2|\n+OG0000990: gi|144227491|gb|AAZ44246.2|\n+OG0000991: gi|144227493|gb|ABO93473.1|\n+OG0000992: gi|71851642|gb|AAZ44250.1|\n+OG0000993: gi|71851676|gb|AAZ44284.1|\n+OG0000994: gi|71851682|gb|AAZ44290.1|\n+OG0000995: gi|144227510|gb|AAZ44298.2|\n+OG0000996: gi|144227520|gb|AAZ44312.2|\n+OG0000997: gi|71851706|gb|AAZ44314.1|\n+OG0000998: gi|144227522|gb|AAZ44315.2|\n+OG0000999: gi|71851710|gb|AAZ44318.1|\n+OG0001000: gi|71851723|gb|AAZ44331.1|\n+OG0001001: gi|144227534|gb|AAZ44338.2|\n+OG0001002: gi|144227542|gb|AAZ44353.2|\n+OG0001003: gi|144227548|gb|AAZ44362.2|\n+OG0001004: gi|71851757|gb|AAZ44365.1|\n+OG0001005: gi|71851762|gb|AAZ44370.1|\n+OG0001006: gi|144227555|gb|AAZ44374.2|\n+OG0001007: gi|71851771|gb|AAZ44379.1|\n+OG0001008: gi|144227557|gb|AAZ44380.2|\n+OG0001009: gi|71851773|gb|AAZ44381.1|\n+OG0001010: gi|144227558|gb|AAZ44382.2|\n+OG0001011: gi|144227559|gb|AAZ44383.2|\n+OG0001012: gi|144227565|gb|AAZ44400.2|\n+OG0001013: gi|144227566|gb|AAZ44401.2|\n+OG0001014: gi|144227567|gb|ABO93475.1|\n+OG0001015: gi|144227572|gb|AAZ44406.2|\n+OG0001016: gi|144227573|gb|AAZ44407.2|\n+OG0001017: gi|144227574|gb|AAZ44408.2|\n+OG0001018: gi|144227576|gb|AAZ44412.2|\n+OG0001019: gi|71851805|gb|AAZ44413.1|\n+OG0001020: gi|144227577|gb|AAZ44414.2|\n+OG0001021: gi|71851809|gb|AAZ44417.1|\n+OG0001022: gi|144227583|gb|ABO93476.1|\n+OG0001023: gi|144227584|gb|AAZ44426.2|\n+OG0001024: gi|144227589|gb|AAZ44431.2|\n+OG0001025: gi|144227590|gb|AAZ44432.2|\n+OG0001026: gi|71851839|gb|AAZ44447.1|\n+OG0001027: gi|144227595|gb|AAZ44448.2|\n+OG0001028: gi|144227606|gb|ABO93477.1|\n+OG0001029: gi|71851862|gb|AAZ44470.1|\n+OG0001030: gi|144227607|gb|ABO93478.1|\n+OG0001031: gi|144227608|gb|AAZ44476.2|\n+OG0001032: gi|71851881|gb|AAZ44489.1|\n+OG0001033: gi|144227616|gb|AAZ44498.2|\n+OG0001034: gi|144227618|gb|AAZ44501.2|\n+OG0001035: gi|71851895|gb|AAZ44503.1|\n+OG0001036: gi|71851899|gb|AAZ44507.1|\n+OG0001037: gi|71851909|gb|AAZ44517.1|\n+OG0001038: gi|144227631|gb|AAZ44526.2|\n+OG0001039: gi|144227633|gb|ABO93479.1|\n+OG0001040: gi|144227635|gb|AAZ44530.2|\n+OG0001041: gi|71851929|gb|AAZ44537.1|\n+OG0001042: gi|144227647|gb|AAZ44549.2|\n+OG0001043: gi|71851956|gb|AAZ44564.1|\n+OG0001044: gi|144227656|gb|AAZ44567.2|\n+OG0001045: gi|144227660|gb|AAZ44572.2|\n+OG0001046: gi|71851966|gb|AAZ44574.1|\n+OG0001047: gi|144227661|gb|AAZ44576.2|\n+OG0001048: gi|71851989|gb|AAZ44597.1|\n+OG0001049: gi|144227669|gb|AAZ44600.2|\n+OG0001050: gi|144227670|gb|AAZ44601.2|\n+OG0001051: gi|144227674|gb|AAZ44606.2|\n+OG0001052: gi|144227675|gb|AAZ44607.2|\n+OG0001053: gi|144227683|gb|AAZ44623.2|\n+OG0001054: gi|144227688|gb|ABO93481.1|\n+OG0001055: gi|144227689|gb|AAZ44632.2|\n+OG0001056: gi|144227690|gb|AAZ44637.2|\n+OG0001057: gi|71852030|gb|AAZ44638.1|\n+OG0001058: gi|144227691|gb|AAZ44639.2|\n+OG0001059: gi|71852032|gb|AAZ44640.1|\n+OG0001060: gi|71852034|gb|AAZ44642.1|\n+OG0001061: gi|144227694|gb|ABO93482.1|\n+OG0001062: gi|144227695|gb|AAZ44645.2|\n+OG0001063: gi|144227698|gb|ABO93483.1|\n+OG0001064: gi|144227699|gb|AAZ44652.2|\n+OG0001065: gi|144227701|gb|AAZ44654.2|\n+OG0001066: gi|144227703|gb|AAZ44657.2|\n+OG0001067: gi|144227704|gb|AAZ44658.2|\n+OG0001068: gi|71852052|gb|AAZ44660.1|\n+OG0001069: gi|144227707|gb|AAZ44671.2|\n+OG0001070: gi|144227709|gb|ABO93484.1|\n+OG0001071: gi|144227725|gb|AAZ44696.2|\n+OG0001072: gi|144227736|gb|AAZ44718.2|\n+OG0001073: gi|71852114|gb|AAZ44722.1|\n+OG0001074: gi|71852141|gb|AAZ44749.1|\n+OG0001075: gi|144227748|gb|AAZ44751.2|\n+OG0001076: gi|71852145|gb|AAZ44753.1|\n+OG0001077: gi|144227749|gb|AAZ44755.2|\n+OG0001078: gi|144227750|gb|AAZ44756.2|\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups_SpeciesOverlaps.csv --- a/test-data/results_fromblast/Orthogroups_SpeciesOverlaps.csv Wed May 13 01:41:06 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ - Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae -Mycoplasma_agalactiae 430 358 302 389 -Mycoplasma_gallisepticum 358 459 383 344 -Mycoplasma_genitalium 302 383 392 294 -Mycoplasma_hyopneumoniae 389 344 294 416 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups_SpeciesOverlaps.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups_SpeciesOverlaps.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ + Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae +Mycoplasma_agalactiae 466 357 301 388 +Mycoplasma_gallisepticum 357 470 381 345 +Mycoplasma_genitalium 301 381 394 294 +Mycoplasma_hyopneumoniae 388 345 294 449 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups_UnassignedGenes.csv --- a/test-data/results_fromblast/Orthogroups_UnassignedGenes.csv Wed May 13 01:41:06 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,796 +0,0 @@\n-\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\r\n-OG0000536\tgi|290752272|emb|CBH40243.1|\t\t\t\r\n-OG0000537\tgi|290752276|emb|CBH40247.1|\t\t\t\r\n-OG0000538\tgi|290752279|emb|CBH40250.1|\t\t\t\r\n-OG0000539\tgi|290752285|emb|CBH40256.1|\t\t\t\r\n-OG0000540\tgi|290752286|emb|CBH40257.1|\t\t\t\r\n-OG0000541\tgi|290752287|emb|CBH40258.1|\t\t\t\r\n-OG0000542\tgi|290752288|emb|CBH40259.1|\t\t\t\r\n-OG0000543\tgi|290752289|emb|CBH40260.1|\t\t\t\r\n-OG0000544\tgi|290752290|emb|CBH40261.1|\t\t\t\r\n-OG0000545\tgi|290752291|emb|CBH40262.1|\t\t\t\r\n-OG0000546\tgi|290752293|emb|CBH40264.1|\t\t\t\r\n-OG0000547\tgi|290752294|emb|CBH40265.1|\t\t\t\r\n-OG0000548\tgi|290752295|emb|CBH40266.1|\t\t\t\r\n-OG0000549\tgi|290752296|emb|CBH40267.1|\t\t\t\r\n-OG0000550\tgi|290752297|emb|CBH40268.1|\t\t\t\r\n-OG0000551\tgi|290752306|emb|CBH40277.1|\t\t\t\r\n-OG0000552\tgi|290752310|emb|CBH40281.1|\t\t\t\r\n-OG0000553\tgi|290752313|emb|CBH40284.1|\t\t\t\r\n-OG0000554\tgi|290752314|emb|CBH40285.1|\t\t\t\r\n-OG0000555\tgi|290752319|emb|CBH40290.1|\t\t\t\r\n-OG0000556\tgi|290752342|emb|CBH40313.1|\t\t\t\r\n-OG0000557\tgi|290752345|emb|CBH40316.1|\t\t\t\r\n-OG0000558\tgi|290752348|emb|CBH40319.1|\t\t\t\r\n-OG0000559\tgi|290752349|emb|CBH40320.1|\t\t\t\r\n-OG0000560\tgi|290752350|emb|CBH40321.1|\t\t\t\r\n-OG0000561\tgi|290752353|emb|CBH40324.1|\t\t\t\r\n-OG0000562\tgi|290752355|emb|CBH40326.1|\t\t\t\r\n-OG0000563\tgi|290752359|emb|CBH40330.1|\t\t\t\r\n-OG0000564\tgi|290752362|emb|CBH40333.1|\t\t\t\r\n-OG0000565\tgi|290752367|emb|CBH40338.1|\t\t\t\r\n-OG0000566\tgi|290752368|emb|CBH40339.1|\t\t\t\r\n-OG0000567\tgi|290752374|emb|CBH40345.1|\t\t\t\r\n-OG0000568\tgi|290752375|emb|CBH40346.1|\t\t\t\r\n-OG0000569\tgi|290752377|emb|CBH40348.1|\t\t\t\r\n-OG0000570\tgi|290752380|emb|CBH40351.1|\t\t\t\r\n-OG0000571\tgi|290752387|emb|CBH40358.1|\t\t\t\r\n-OG0000572\tgi|290752389|emb|CBH40360.1|\t\t\t\r\n-OG0000573\tgi|290752396|emb|CBH40367.1|\t\t\t\r\n-OG0000574\tgi|290752398|emb|CBH40369.1|\t\t\t\r\n-OG0000575\tgi|290752399|emb|CBH40370.1|\t\t\t\r\n-OG0000576\tgi|290752400|emb|CBH40371.1|\t\t\t\r\n-OG0000577\tgi|290752405|emb|CBH40376.1|\t\t\t\r\n-OG0000578\tgi|290752407|emb|CBH40378.1|\t\t\t\r\n-OG0000579\tgi|290752409|emb|CBH40380.1|\t\t\t\r\n-OG0000580\tgi|290752411|emb|CBH40382.1|\t\t\t\r\n-OG0000581\tgi|290752412|emb|CBH40383.1|\t\t\t\r\n-OG0000582\tgi|290752413|emb|CBH40384.1|\t\t\t\r\n-OG0000583\tgi|290752415|emb|CBH40386.1|\t\t\t\r\n-OG0000584\tgi|290752417|emb|CBH40388.1|\t\t\t\r\n-OG0000585\tgi|290752419|emb|CBH40390.1|\t\t\t\r\n-OG0000586\tgi|290752421|emb|CBH40392.1|\t\t\t\r\n-OG0000587\tgi|290752423|emb|CBH40394.1|\t\t\t\r\n-OG0000588\tgi|290752424|emb|CBH40395.1|\t\t\t\r\n-OG0000589\tgi|290752425|emb|CBH40396.1|\t\t\t\r\n-OG0000590\tgi|290752428|emb|CBH40399.1|\t\t\t\r\n-OG0000591\tgi|290752429|emb|CBH40400.1|\t\t\t\r\n-OG0000592\tgi|290752430|emb|CBH40401.1|\t\t\t\r\n-OG0000593\tgi|290752432|emb|CBH40403.1|\t\t\t\r\n-OG0000594\tgi|290752436|emb|CBH40407.1|\t\t\t\r\n-OG0000595\tgi|290752439|emb|CBH40410.1|\t\t\t\r\n-OG0000596\tgi|290752444|emb|CBH40415.1|\t\t\t\r\n-OG0000597\tgi|290752447|emb|CBH40418.1|\t\t\t\r\n-OG0000598\tgi|290752448|emb|CBH40420.1|\t\t\t\r\n-OG0000599\tgi|290752449|emb|CBH40421.1|\t\t\t\r\n-OG0000600\tgi|290752453|emb|CBH40425.1|\t\t\t\r\n-OG0000601\tgi|290752457|emb|CBH40429.1|\t\t\t\r\n-OG0000602\tgi|290752462|emb|CBH40434.1|\t\t\t\r\n-OG0000603\tgi|290752466|emb|CBH40438.1|\t\t\t\r\n-OG0000604\tgi|290752472|emb|CBH40444.1|\t\t\t\r\n-OG0000605\tgi|290752473|emb|CBH40445.1|\t\t\t\r\n-OG0000606\tgi|290752474|emb|CBH40446.1|\t\t\t\r\n-OG0000607\tgi|290752475|emb|CBH40447.1|\t\t\t\r\n-OG0000608\tgi|290752476|emb|CBH40448.1|\t\t\t\r\n-OG0000609\tgi|290752495|emb|CBH40467.1|\t\t\t\r\n-OG0000610\tgi|290752500|emb|CBH40472.1|\t\t\t\r\n-OG0000611\tgi|290752502|emb|CBH40474.1|\t\t\t\r\n-OG0000612\tgi|290752505|emb|CBH40477.1|\t\t\t\r\n-OG0000613\tgi|290752506|emb|CBH40478.1|\t\t\t\r\n-OG0000614\tgi|290752507|emb|CBH40479.1|\t\t\t\r\n-OG0000615\tgi|290752509|emb|CBH40481.1|\t\t\t\r\n-OG0000616\tgi|290752510|emb|CBH40482.1|\t\t\t\r\n-OG0000617\tgi|290752511|emb|CBH40483.1|\t\t\t\r\n-OG0000618\tgi|290752512|emb|CBH40484.1|\t\t\t\r\n-OG0000619\tgi|290752514|emb|CBH40486.1|\t\t\t\r\n-OG0000620\tgi|290752517|emb|CBH40489.1|\t\t\t\r\n-OG0000621\tgi|290752524|emb|CBH40496.1|\t\t\t\r\n-OG0000622\tgi|290752528|emb|CBH40500.1|\t\t\t\r\n-OG0000623\tgi|290752537|emb|CBH40509.1|\t\t\t\r\n-OG0000624\tg'..b'\t\t\t\tgi|71851900|gb|AAZ44508.1|\r\n-OG0001238\t\t\t\tgi|71851902|gb|AAZ44510.1|\r\n-OG0001239\t\t\t\tgi|144227625|gb|AAZ44516.2|\r\n-OG0001240\t\t\t\tgi|71851909|gb|AAZ44517.1|\r\n-OG0001241\t\t\t\tgi|144227629|gb|AAZ44523.2|\r\n-OG0001242\t\t\t\tgi|144227630|gb|AAZ44524.2|\r\n-OG0001243\t\t\t\tgi|144227631|gb|AAZ44526.2|\r\n-OG0001244\t\t\t\tgi|144227632|gb|AAZ44527.2|\r\n-OG0001245\t\t\t\tgi|144227633|gb|ABO93479.1|\r\n-OG0001246\t\t\t\tgi|144227634|gb|AAZ44528.2|\r\n-OG0001247\t\t\t\tgi|71851921|gb|AAZ44529.1|\r\n-OG0001248\t\t\t\tgi|144227635|gb|AAZ44530.2|\r\n-OG0001249\t\t\t\tgi|144227636|gb|AAZ44531.2|\r\n-OG0001250\t\t\t\tgi|71851929|gb|AAZ44537.1|\r\n-OG0001251\t\t\t\tgi|71851936|gb|AAZ44544.1|\r\n-OG0001252\t\t\t\tgi|144227644|gb|AAZ44545.2|\r\n-OG0001253\t\t\t\tgi|144227645|gb|AAZ44546.2|\r\n-OG0001254\t\t\t\tgi|144227647|gb|AAZ44549.2|\r\n-OG0001255\t\t\t\tgi|144227650|gb|AAZ44554.2|\r\n-OG0001256\t\t\t\tgi|71851956|gb|AAZ44564.1|\r\n-OG0001257\t\t\t\tgi|144227656|gb|AAZ44567.2|\r\n-OG0001258\t\t\t\tgi|144227660|gb|AAZ44572.2|\r\n-OG0001259\t\t\t\tgi|71851966|gb|AAZ44574.1|\r\n-OG0001260\t\t\t\tgi|144227661|gb|AAZ44576.2|\r\n-OG0001261\t\t\t\tgi|71851971|gb|AAZ44579.1|\r\n-OG0001262\t\t\t\tgi|71851972|gb|AAZ44580.1|\r\n-OG0001263\t\t\t\tgi|71851985|gb|AAZ44593.1|\r\n-OG0001264\t\t\t\tgi|71851986|gb|AAZ44594.1|\r\n-OG0001265\t\t\t\tgi|144227667|gb|AAZ44595.2|\r\n-OG0001266\t\t\t\tgi|71851988|gb|AAZ44596.1|\r\n-OG0001267\t\t\t\tgi|71851989|gb|AAZ44597.1|\r\n-OG0001268\t\t\t\tgi|144227668|gb|AAZ44598.2|\r\n-OG0001269\t\t\t\tgi|71851991|gb|AAZ44599.1|\r\n-OG0001270\t\t\t\tgi|144227669|gb|AAZ44600.2|\r\n-OG0001271\t\t\t\tgi|144227670|gb|AAZ44601.2|\r\n-OG0001272\t\t\t\tgi|144227671|gb|AAZ44602.2|\r\n-OG0001273\t\t\t\tgi|144227672|gb|AAZ44604.2|\r\n-OG0001274\t\t\t\tgi|144227673|gb|AAZ44605.2|\r\n-OG0001275\t\t\t\tgi|144227674|gb|AAZ44606.2|\r\n-OG0001276\t\t\t\tgi|144227675|gb|AAZ44607.2|\r\n-OG0001277\t\t\t\tgi|144227676|gb|ABO93480.1|\r\n-OG0001278\t\t\t\tgi|144227681|gb|AAZ44617.2|\r\n-OG0001279\t\t\t\tgi|144227683|gb|AAZ44623.2|\r\n-OG0001280\t\t\t\tgi|144227688|gb|ABO93481.1|\r\n-OG0001281\t\t\t\tgi|144227689|gb|AAZ44632.2|\r\n-OG0001282\t\t\t\tgi|71852025|gb|AAZ44633.1|\r\n-OG0001283\t\t\t\tgi|144227690|gb|AAZ44637.2|\r\n-OG0001284\t\t\t\tgi|71852030|gb|AAZ44638.1|\r\n-OG0001285\t\t\t\tgi|144227691|gb|AAZ44639.2|\r\n-OG0001286\t\t\t\tgi|71852032|gb|AAZ44640.1|\r\n-OG0001287\t\t\t\tgi|71852034|gb|AAZ44642.1|\r\n-OG0001288\t\t\t\tgi|71852035|gb|AAZ44643.1|\r\n-OG0001289\t\t\t\tgi|144227693|gb|AAZ44644.2|\r\n-OG0001290\t\t\t\tgi|144227694|gb|ABO93482.1|\r\n-OG0001291\t\t\t\tgi|144227695|gb|AAZ44645.2|\r\n-OG0001292\t\t\t\tgi|71852038|gb|AAZ44646.1|\r\n-OG0001293\t\t\t\tgi|144227696|gb|AAZ44647.2|\r\n-OG0001294\t\t\t\tgi|71852040|gb|AAZ44648.1|\r\n-OG0001295\t\t\t\tgi|144227697|gb|AAZ44650.2|\r\n-OG0001296\t\t\t\tgi|71852043|gb|AAZ44651.1|\r\n-OG0001297\t\t\t\tgi|144227698|gb|ABO93483.1|\r\n-OG0001298\t\t\t\tgi|144227699|gb|AAZ44652.2|\r\n-OG0001299\t\t\t\tgi|144227700|gb|AAZ44653.2|\r\n-OG0001300\t\t\t\tgi|144227701|gb|AAZ44654.2|\r\n-OG0001301\t\t\t\tgi|71852048|gb|AAZ44656.1|\r\n-OG0001302\t\t\t\tgi|144227703|gb|AAZ44657.2|\r\n-OG0001303\t\t\t\tgi|144227704|gb|AAZ44658.2|\r\n-OG0001304\t\t\t\tgi|71852052|gb|AAZ44660.1|\r\n-OG0001305\t\t\t\tgi|144227707|gb|AAZ44671.2|\r\n-OG0001306\t\t\t\tgi|144227709|gb|ABO93484.1|\r\n-OG0001307\t\t\t\tgi|144227715|gb|AAZ44680.2|\r\n-OG0001308\t\t\t\tgi|144227716|gb|AAZ44681.2|\r\n-OG0001309\t\t\t\tgi|144227717|gb|AAZ44682.2|\r\n-OG0001310\t\t\t\tgi|71852075|gb|AAZ44683.1|\r\n-OG0001311\t\t\t\tgi|144227718|gb|AAZ44684.2|\r\n-OG0001312\t\t\t\tgi|71852077|gb|AAZ44685.1|\r\n-OG0001313\t\t\t\tgi|144227719|gb|AAZ44686.2|\r\n-OG0001314\t\t\t\tgi|144227725|gb|AAZ44696.2|\r\n-OG0001315\t\t\t\tgi|144227730|gb|AAZ44708.2|\r\n-OG0001316\t\t\t\tgi|71852101|gb|AAZ44709.1|\r\n-OG0001317\t\t\t\tgi|144227731|gb|AAZ44711.2|\r\n-OG0001318\t\t\t\tgi|144227732|gb|AAZ44712.2|\r\n-OG0001319\t\t\t\tgi|144227736|gb|AAZ44718.2|\r\n-OG0001320\t\t\t\tgi|71852114|gb|AAZ44722.1|\r\n-OG0001321\t\t\t\tgi|144227745|gb|AAZ44743.2|\r\n-OG0001322\t\t\t\tgi|144227746|gb|AAZ44744.2|\r\n-OG0001323\t\t\t\tgi|144227747|gb|AAZ44745.2|\r\n-OG0001324\t\t\t\tgi|71852138|gb|AAZ44746.1|\r\n-OG0001325\t\t\t\tgi|71852139|gb|AAZ44747.1|\r\n-OG0001326\t\t\t\tgi|71852141|gb|AAZ44749.1|\r\n-OG0001327\t\t\t\tgi|144227748|gb|AAZ44751.2|\r\n-OG0001328\t\t\t\tgi|71852145|gb|AAZ44753.1|\r\n-OG0001329\t\t\t\tgi|144227749|gb|AAZ44755.2|\r\n-OG0001330\t\t\t\tgi|144227750|gb|AAZ44756.2|\r\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Orthogroups_UnassignedGenes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Orthogroups_UnassignedGenes.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| b'@@ -0,0 +1,458 @@\n+Orthogroup\tMycoplasma_agalactiae\tMycoplasma_gallisepticum\tMycoplasma_genitalium\tMycoplasma_hyopneumoniae\n+OG0000622\tgi|290752272|emb|CBH40243.1|\t\t\t\n+OG0000623\tgi|290752276|emb|CBH40247.1|\t\t\t\n+OG0000624\tgi|290752290|emb|CBH40261.1|\t\t\t\n+OG0000625\tgi|290752291|emb|CBH40262.1|\t\t\t\n+OG0000626\tgi|290752294|emb|CBH40265.1|\t\t\t\n+OG0000627\tgi|290752296|emb|CBH40267.1|\t\t\t\n+OG0000628\tgi|290752297|emb|CBH40268.1|\t\t\t\n+OG0000629\tgi|290752306|emb|CBH40277.1|\t\t\t\n+OG0000630\tgi|290752310|emb|CBH40281.1|\t\t\t\n+OG0000631\tgi|290752313|emb|CBH40284.1|\t\t\t\n+OG0000632\tgi|290752314|emb|CBH40285.1|\t\t\t\n+OG0000633\tgi|290752319|emb|CBH40290.1|\t\t\t\n+OG0000634\tgi|290752342|emb|CBH40313.1|\t\t\t\n+OG0000635\tgi|290752345|emb|CBH40316.1|\t\t\t\n+OG0000636\tgi|290752348|emb|CBH40319.1|\t\t\t\n+OG0000637\tgi|290752350|emb|CBH40321.1|\t\t\t\n+OG0000638\tgi|290752353|emb|CBH40324.1|\t\t\t\n+OG0000639\tgi|290752355|emb|CBH40326.1|\t\t\t\n+OG0000640\tgi|290752359|emb|CBH40330.1|\t\t\t\n+OG0000641\tgi|290752362|emb|CBH40333.1|\t\t\t\n+OG0000642\tgi|290752367|emb|CBH40338.1|\t\t\t\n+OG0000643\tgi|290752374|emb|CBH40345.1|\t\t\t\n+OG0000644\tgi|290752375|emb|CBH40346.1|\t\t\t\n+OG0000645\tgi|290752377|emb|CBH40348.1|\t\t\t\n+OG0000646\tgi|290752380|emb|CBH40351.1|\t\t\t\n+OG0000647\tgi|290752387|emb|CBH40358.1|\t\t\t\n+OG0000648\tgi|290752389|emb|CBH40360.1|\t\t\t\n+OG0000649\tgi|290752396|emb|CBH40367.1|\t\t\t\n+OG0000650\tgi|290752398|emb|CBH40369.1|\t\t\t\n+OG0000651\tgi|290752400|emb|CBH40371.1|\t\t\t\n+OG0000652\tgi|290752405|emb|CBH40376.1|\t\t\t\n+OG0000653\tgi|290752407|emb|CBH40378.1|\t\t\t\n+OG0000654\tgi|290752411|emb|CBH40382.1|\t\t\t\n+OG0000655\tgi|290752412|emb|CBH40383.1|\t\t\t\n+OG0000656\tgi|290752413|emb|CBH40384.1|\t\t\t\n+OG0000657\tgi|290752424|emb|CBH40395.1|\t\t\t\n+OG0000658\tgi|290752425|emb|CBH40396.1|\t\t\t\n+OG0000659\tgi|290752436|emb|CBH40407.1|\t\t\t\n+OG0000660\tgi|290752439|emb|CBH40410.1|\t\t\t\n+OG0000661\tgi|290752444|emb|CBH40415.1|\t\t\t\n+OG0000662\tgi|290752449|emb|CBH40421.1|\t\t\t\n+OG0000663\tgi|290752453|emb|CBH40425.1|\t\t\t\n+OG0000664\tgi|290752457|emb|CBH40429.1|\t\t\t\n+OG0000665\tgi|290752462|emb|CBH40434.1|\t\t\t\n+OG0000666\tgi|290752466|emb|CBH40438.1|\t\t\t\n+OG0000667\tgi|290752474|emb|CBH40446.1|\t\t\t\n+OG0000668\tgi|290752476|emb|CBH40448.1|\t\t\t\n+OG0000669\tgi|290752506|emb|CBH40478.1|\t\t\t\n+OG0000670\tgi|290752507|emb|CBH40479.1|\t\t\t\n+OG0000671\tgi|290752510|emb|CBH40482.1|\t\t\t\n+OG0000672\tgi|290752511|emb|CBH40483.1|\t\t\t\n+OG0000673\tgi|290752514|emb|CBH40486.1|\t\t\t\n+OG0000674\tgi|290752528|emb|CBH40500.1|\t\t\t\n+OG0000675\tgi|290752537|emb|CBH40509.1|\t\t\t\n+OG0000676\tgi|290752568|emb|CBH40540.1|\t\t\t\n+OG0000677\tgi|290752575|emb|CBH40547.1|\t\t\t\n+OG0000678\tgi|290752576|emb|CBH40548.1|\t\t\t\n+OG0000679\tgi|290752578|emb|CBH40550.1|\t\t\t\n+OG0000680\tgi|290752579|emb|CBH40551.1|\t\t\t\n+OG0000681\tgi|290752581|emb|CBH40553.1|\t\t\t\n+OG0000682\tgi|290752582|emb|CBH40554.1|\t\t\t\n+OG0000683\tgi|290752585|emb|CBH40557.1|\t\t\t\n+OG0000684\tgi|290752588|emb|CBH40560.1|\t\t\t\n+OG0000685\tgi|290752595|emb|CBH40567.1|\t\t\t\n+OG0000686\tgi|290752598|emb|CBH40570.1|\t\t\t\n+OG0000687\tgi|290752599|emb|CBH40571.1|\t\t\t\n+OG0000688\tgi|290752605|emb|CBH40577.1|\t\t\t\n+OG0000689\tgi|290752607|emb|CBH40579.1|\t\t\t\n+OG0000690\tgi|290752613|emb|CBH40585.1|\t\t\t\n+OG0000691\tgi|290752614|emb|CBH40586.1|\t\t\t\n+OG0000692\tgi|290752615|emb|CBH40587.1|\t\t\t\n+OG0000693\tgi|290752621|emb|CBH40594.1|\t\t\t\n+OG0000694\tgi|290752624|emb|CBH40597.1|\t\t\t\n+OG0000695\tgi|290752625|emb|CBH40598.1|\t\t\t\n+OG0000696\tgi|290752633|emb|CBH40606.1|\t\t\t\n+OG0000697\tgi|290752634|emb|CBH40607.1|\t\t\t\n+OG0000698\tgi|290752635|emb|CBH40608.1|\t\t\t\n+OG0000699\tgi|290752637|emb|CBH40610.1|\t\t\t\n+OG0000700\tgi|290752642|emb|CBH40615.1|\t\t\t\n+OG0000701\tgi|290752645|emb|CBH40618.1|\t\t\t\n+OG0000702\tgi|290752646|emb|CBH40619.1|\t\t\t\n+OG0000703\tgi|290752654|emb|CBH40627.1|\t\t\t\n+OG0000704\tgi|290752657|emb|CBH40630.1|\t\t\t\n+OG0000705\tgi|290752659|emb|CBH40632.1|\t\t\t\n+OG0000706\tgi|290752666|emb|CBH40639.1|\t\t\t\n+OG0000707\tgi|290752669|emb|CBH40642.1|\t\t\t\n+OG0000708\tgi|290752672|emb|CBH40645.1|\t\t\t\n+OG0000709\tgi|290752675|emb|CBH40648.1|\t\t\t\n+OG0000710\tgi|290752677|emb|CBH40650.1|\t\t\t\n+OG0000711\tgi|290752682|emb|CBH40655.1|\t\t\t\n+OG00'..b'OG0000983\t\t\t\tgi|71851587|gb|AAZ44195.1|\n+OG0000984\t\t\t\tgi|71851592|gb|AAZ44200.1|\n+OG0000985\t\t\t\tgi|144227472|gb|AAZ44207.2|\n+OG0000986\t\t\t\tgi|71851608|gb|AAZ44216.1|\n+OG0000987\t\t\t\tgi|144227481|gb|AAZ44225.2|\n+OG0000988\t\t\t\tgi|144227484|gb|AAZ44229.2|\n+OG0000989\t\t\t\tgi|144227489|gb|AAZ44237.2|\n+OG0000990\t\t\t\tgi|144227491|gb|AAZ44246.2|\n+OG0000991\t\t\t\tgi|144227493|gb|ABO93473.1|\n+OG0000992\t\t\t\tgi|71851642|gb|AAZ44250.1|\n+OG0000993\t\t\t\tgi|71851676|gb|AAZ44284.1|\n+OG0000994\t\t\t\tgi|71851682|gb|AAZ44290.1|\n+OG0000995\t\t\t\tgi|144227510|gb|AAZ44298.2|\n+OG0000996\t\t\t\tgi|144227520|gb|AAZ44312.2|\n+OG0000997\t\t\t\tgi|71851706|gb|AAZ44314.1|\n+OG0000998\t\t\t\tgi|144227522|gb|AAZ44315.2|\n+OG0000999\t\t\t\tgi|71851710|gb|AAZ44318.1|\n+OG0001000\t\t\t\tgi|71851723|gb|AAZ44331.1|\n+OG0001001\t\t\t\tgi|144227534|gb|AAZ44338.2|\n+OG0001002\t\t\t\tgi|144227542|gb|AAZ44353.2|\n+OG0001003\t\t\t\tgi|144227548|gb|AAZ44362.2|\n+OG0001004\t\t\t\tgi|71851757|gb|AAZ44365.1|\n+OG0001005\t\t\t\tgi|71851762|gb|AAZ44370.1|\n+OG0001006\t\t\t\tgi|144227555|gb|AAZ44374.2|\n+OG0001007\t\t\t\tgi|71851771|gb|AAZ44379.1|\n+OG0001008\t\t\t\tgi|144227557|gb|AAZ44380.2|\n+OG0001009\t\t\t\tgi|71851773|gb|AAZ44381.1|\n+OG0001010\t\t\t\tgi|144227558|gb|AAZ44382.2|\n+OG0001011\t\t\t\tgi|144227559|gb|AAZ44383.2|\n+OG0001012\t\t\t\tgi|144227565|gb|AAZ44400.2|\n+OG0001013\t\t\t\tgi|144227566|gb|AAZ44401.2|\n+OG0001014\t\t\t\tgi|144227567|gb|ABO93475.1|\n+OG0001015\t\t\t\tgi|144227572|gb|AAZ44406.2|\n+OG0001016\t\t\t\tgi|144227573|gb|AAZ44407.2|\n+OG0001017\t\t\t\tgi|144227574|gb|AAZ44408.2|\n+OG0001018\t\t\t\tgi|144227576|gb|AAZ44412.2|\n+OG0001019\t\t\t\tgi|71851805|gb|AAZ44413.1|\n+OG0001020\t\t\t\tgi|144227577|gb|AAZ44414.2|\n+OG0001021\t\t\t\tgi|71851809|gb|AAZ44417.1|\n+OG0001022\t\t\t\tgi|144227583|gb|ABO93476.1|\n+OG0001023\t\t\t\tgi|144227584|gb|AAZ44426.2|\n+OG0001024\t\t\t\tgi|144227589|gb|AAZ44431.2|\n+OG0001025\t\t\t\tgi|144227590|gb|AAZ44432.2|\n+OG0001026\t\t\t\tgi|71851839|gb|AAZ44447.1|\n+OG0001027\t\t\t\tgi|144227595|gb|AAZ44448.2|\n+OG0001028\t\t\t\tgi|144227606|gb|ABO93477.1|\n+OG0001029\t\t\t\tgi|71851862|gb|AAZ44470.1|\n+OG0001030\t\t\t\tgi|144227607|gb|ABO93478.1|\n+OG0001031\t\t\t\tgi|144227608|gb|AAZ44476.2|\n+OG0001032\t\t\t\tgi|71851881|gb|AAZ44489.1|\n+OG0001033\t\t\t\tgi|144227616|gb|AAZ44498.2|\n+OG0001034\t\t\t\tgi|144227618|gb|AAZ44501.2|\n+OG0001035\t\t\t\tgi|71851895|gb|AAZ44503.1|\n+OG0001036\t\t\t\tgi|71851899|gb|AAZ44507.1|\n+OG0001037\t\t\t\tgi|71851909|gb|AAZ44517.1|\n+OG0001038\t\t\t\tgi|144227631|gb|AAZ44526.2|\n+OG0001039\t\t\t\tgi|144227633|gb|ABO93479.1|\n+OG0001040\t\t\t\tgi|144227635|gb|AAZ44530.2|\n+OG0001041\t\t\t\tgi|71851929|gb|AAZ44537.1|\n+OG0001042\t\t\t\tgi|144227647|gb|AAZ44549.2|\n+OG0001043\t\t\t\tgi|71851956|gb|AAZ44564.1|\n+OG0001044\t\t\t\tgi|144227656|gb|AAZ44567.2|\n+OG0001045\t\t\t\tgi|144227660|gb|AAZ44572.2|\n+OG0001046\t\t\t\tgi|71851966|gb|AAZ44574.1|\n+OG0001047\t\t\t\tgi|144227661|gb|AAZ44576.2|\n+OG0001048\t\t\t\tgi|71851989|gb|AAZ44597.1|\n+OG0001049\t\t\t\tgi|144227669|gb|AAZ44600.2|\n+OG0001050\t\t\t\tgi|144227670|gb|AAZ44601.2|\n+OG0001051\t\t\t\tgi|144227674|gb|AAZ44606.2|\n+OG0001052\t\t\t\tgi|144227675|gb|AAZ44607.2|\n+OG0001053\t\t\t\tgi|144227683|gb|AAZ44623.2|\n+OG0001054\t\t\t\tgi|144227688|gb|ABO93481.1|\n+OG0001055\t\t\t\tgi|144227689|gb|AAZ44632.2|\n+OG0001056\t\t\t\tgi|144227690|gb|AAZ44637.2|\n+OG0001057\t\t\t\tgi|71852030|gb|AAZ44638.1|\n+OG0001058\t\t\t\tgi|144227691|gb|AAZ44639.2|\n+OG0001059\t\t\t\tgi|71852032|gb|AAZ44640.1|\n+OG0001060\t\t\t\tgi|71852034|gb|AAZ44642.1|\n+OG0001061\t\t\t\tgi|144227694|gb|ABO93482.1|\n+OG0001062\t\t\t\tgi|144227695|gb|AAZ44645.2|\n+OG0001063\t\t\t\tgi|144227698|gb|ABO93483.1|\n+OG0001064\t\t\t\tgi|144227699|gb|AAZ44652.2|\n+OG0001065\t\t\t\tgi|144227701|gb|AAZ44654.2|\n+OG0001066\t\t\t\tgi|144227703|gb|AAZ44657.2|\n+OG0001067\t\t\t\tgi|144227704|gb|AAZ44658.2|\n+OG0001068\t\t\t\tgi|71852052|gb|AAZ44660.1|\n+OG0001069\t\t\t\tgi|144227707|gb|AAZ44671.2|\n+OG0001070\t\t\t\tgi|144227709|gb|ABO93484.1|\n+OG0001071\t\t\t\tgi|144227725|gb|AAZ44696.2|\n+OG0001072\t\t\t\tgi|144227736|gb|AAZ44718.2|\n+OG0001073\t\t\t\tgi|71852114|gb|AAZ44722.1|\n+OG0001074\t\t\t\tgi|71852141|gb|AAZ44749.1|\n+OG0001075\t\t\t\tgi|144227748|gb|AAZ44751.2|\n+OG0001076\t\t\t\tgi|71852145|gb|AAZ44753.1|\n+OG0001077\t\t\t\tgi|144227749|gb|AAZ44755.2|\n+OG0001078\t\t\t\tgi|144227750|gb|AAZ44756.2|\n' |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Statistics_Overall.csv --- a/test-data/results_fromblast/Statistics_Overall.csv Wed May 13 01:41:06 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,51 +0,0 @@ -Number of genes 2733 -Number of genes in orthogroups 1938 -Number of unassigned genes 795 -Percentage of genes in orthogroups 70.9 -Percentage of unassigned genes 29.1 -Number of orthogroups 536 -Number of species-specific orthogroups 6 -Number of genes in species-specific orthogroups 100 -Percentage of genes in species-specific orthogroups 3.7 -Mean orthogroup size 3.6 -Median orthogroup size 4.0 -G50 (assigned genes) 4 -G50 (all genes) 4 -O50 (assigned genes) 199 -O50 (all genes) 299 -Number of orthogroups with all species present 278 -Number of single-copy orthogroups 254 -Date 2017-06-08 -Orthogroups file Orthogroups.csv -Unassigned genes file Orthogroups_UnassignedGenes.csv -Per-species statistics Statistics_PerSpecies.csv -Overall statistics Statistics_Overall.csv -Orthogroups shared between species Orthogroups_SpeciesOverlaps.csv - -Average number of genes per-species in orthogroup Number of orthogroups Percentage of orthogroups Number of genes Percentage of genes -<1 224 41.8 516 26.6 -'1 302 56.3 1254 64.7 -'2 7 1.3 65 3.4 -'3 0 0.0 0 0.0 -'4 0 0.0 0 0.0 -'5 1 0.2 20 1.0 -'6 1 0.2 27 1.4 -'7 0 0.0 0 0.0 -'8 0 0.0 0 0.0 -'9 0 0.0 0 0.0 -'10 0 0.0 0 0.0 -11-15 1 0.2 56 2.9 -16-20 0 0.0 0 0.0 -21-50 0 0.0 0 0.0 -51-100 0 0.0 0 0.0 -101-150 0 0.0 0 0.0 -151-200 0 0.0 0 0.0 -201-500 0 0.0 0 0.0 -501-1000 0 0.0 0 0.0 -'1001+ 0 0.0 0 0.0 - -Number of species in orthogroup Number of orthogroups -1 6 -2 177 -3 75 -4 278 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Statistics_Overall.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Statistics_Overall.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,52 @@ +Number of species 4 +Number of genes 2733 +Number of genes in orthogroups 2276 +Number of unassigned genes 457 +Percentage of genes in orthogroups 83.3 +Percentage of unassigned genes 16.7 +Number of orthogroups 622 +Number of species-specific orthogroups 96 +Number of genes in species-specific orthogroups 426 +Percentage of genes in species-specific orthogroups 15.6 +Mean orthogroup size 3.7 +Median orthogroup size 4.0 +G50 (assigned genes) 4 +G50 (all genes) 4 +O50 (assigned genes) 221 +O50 (all genes) 278 +Number of orthogroups with all species present 278 +Number of single-copy orthogroups 249 +Date 2020-08-14 +Orthogroups file Orthogroups.tsv +Unassigned genes file Orthogroups_UnassignedGenes.tsv +Per-species statistics Statistics_PerSpecies.tsv +Overall statistics Statistics_Overall.tsv +Orthogroups shared between species Orthogroups_SpeciesOverlaps.tsv + +Average number of genes per-species in orthogroup Number of orthogroups Percentage of orthogroups Number of genes Percentage of genes +<1 285 45.8 672 29.5 +'1 322 51.8 1352 59.4 +'2 8 1.3 73 3.2 +'3 4 0.6 56 2.5 +'4 0 0.0 0 0.0 +'5 0 0.0 0 0.0 +'6 1 0.2 26 1.1 +'7 0 0.0 0 0.0 +'8 0 0.0 0 0.0 +'9 1 0.2 39 1.7 +'10 0 0.0 0 0.0 +11-15 1 0.2 58 2.5 +16-20 0 0.0 0 0.0 +21-50 0 0.0 0 0.0 +51-100 0 0.0 0 0.0 +101-150 0 0.0 0 0.0 +151-200 0 0.0 0 0.0 +201-500 0 0.0 0 0.0 +501-1000 0 0.0 0 0.0 +'1001+ 0 0.0 0 0.0 + +Number of species in orthogroup Number of orthogroups +1 96 +2 173 +3 75 +4 278 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Statistics_PerSpecies.csv --- a/test-data/results_fromblast/Statistics_PerSpecies.csv Wed May 13 01:41:06 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,100 +0,0 @@ - Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae -Number of genes 820 763 476 674 -Number of genes in orthogroups 503 561 429 445 -Number of unassigned genes 317 202 47 229 -Percentage of genes in orthogroups 61.3 73.5 90.1 66.0 -Percentage of unassigned genes 38.7 26.5 9.9 34.0 -Number of orthogroups containing species 430 459 392 416 -Percentage of orthogroups containing species 80.2 85.6 73.1 77.6 -Number of species-specific orthogroups 3 2 0 1 -Number of genes in species-specific orthogroups 34 61 0 5 -Percentage of genes in species-specific orthogroups 4.1 8.0 0.0 0.7 - - -Number of genes per-species in orthogroup Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups -'0 106 77 144 120 -'1 398 427 368 405 -'2 21 21 17 6 -'3 6 6 5 1 -'4 2 2 1 1 -'5 2 2 0 1 -'6 0 0 0 0 -'7 0 0 0 0 -'8 0 0 1 2 -'9 0 0 0 0 -'10 0 0 0 0 -11-15 0 0 0 0 -16-20 0 0 0 0 -21-50 1 0 0 0 -51-100 0 1 0 0 -101-150 0 0 0 0 -151-200 0 0 0 0 -201-500 0 0 0 0 -501-1000 0 0 0 0 -'1001+ 0 0 0 0 - -Number of genes per-species in orthogroup Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups -'0 19.8 14.4 26.9 22.4 -'1 74.3 79.7 68.7 75.6 -'2 3.9 3.9 3.2 1.1 -'3 1.1 1.1 0.9 0.2 -'4 0.4 0.4 0.2 0.2 -'5 0.4 0.4 0.0 0.2 -'6 0.0 0.0 0.0 0.0 -'7 0.0 0.0 0.0 0.0 -'8 0.0 0.0 0.2 0.4 -'9 0.0 0.0 0.0 0.0 -'10 0.0 0.0 0.0 0.0 -11-15 0.0 0.0 0.0 0.0 -16-20 0.0 0.0 0.0 0.0 -21-50 0.2 0.0 0.0 0.0 -51-100 0.0 0.2 0.0 0.0 -101-150 0.0 0.0 0.0 0.0 -151-200 0.0 0.0 0.0 0.0 -201-500 0.0 0.0 0.0 0.0 -501-1000 0.0 0.0 0.0 0.0 -'1001+ 0.0 0.0 0.0 0.0 - -Number of genes per-species in orthogroup Number of genes Number of genes Number of genes Number of genes -'0 0 0 0 0 -'1 398 427 368 405 -'2 42 42 34 12 -'3 18 18 15 3 -'4 8 8 4 4 -'5 10 10 0 5 -'6 0 0 0 0 -'7 0 0 0 0 -'8 0 0 8 16 -'9 0 0 0 0 -'10 0 0 0 0 -11-15 0 0 0 0 -16-20 0 0 0 0 -21-50 27 0 0 0 -51-100 0 56 0 0 -101-150 0 0 0 0 -151-200 0 0 0 0 -201-500 0 0 0 0 -501-1000 0 0 0 0 -'1001+ 0 0 0 0 - -Number of genes per-species in orthogroup Percentage of genes Percentage of genes Percentage of genes Percentage of genes -'0 0.0 0.0 0.0 0.0 -'1 48.5 56.0 77.3 60.1 -'2 5.1 5.5 7.1 1.8 -'3 2.2 2.4 3.2 0.4 -'4 1.0 1.0 0.8 0.6 -'5 1.2 1.3 0.0 0.7 -'6 0.0 0.0 0.0 0.0 -'7 0.0 0.0 0.0 0.0 -'8 0.0 0.0 1.7 2.4 -'9 0.0 0.0 0.0 0.0 -'10 0.0 0.0 0.0 0.0 -11-15 0.0 0.0 0.0 0.0 -16-20 0.0 0.0 0.0 0.0 -21-50 3.3 0.0 0.0 0.0 -51-100 0.0 7.3 0.0 0.0 -101-150 0.0 0.0 0.0 0.0 -151-200 0.0 0.0 0.0 0.0 -201-500 0.0 0.0 0.0 0.0 -501-1000 0.0 0.0 0.0 0.0 -'1001+ 0.0 0.0 0.0 0.0 |
| b |
| diff -r 999060f051ac -r 974d8c28e586 test-data/results_fromblast/Statistics_PerSpecies.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_fromblast/Statistics_PerSpecies.tsv Mon Aug 17 12:59:19 2020 -0400 |
| b |
| @@ -0,0 +1,100 @@ + Mycoplasma_agalactiae Mycoplasma_gallisepticum Mycoplasma_genitalium Mycoplasma_hyopneumoniae +Number of genes 820 763 476 674 +Number of genes in orthogroups 659 619 436 562 +Number of unassigned genes 161 144 40 112 +Percentage of genes in orthogroups 80.4 81.1 91.6 83.4 +Percentage of unassigned genes 19.6 18.9 8.4 16.6 +Number of orthogroups containing species 466 470 394 449 +Percentage of orthogroups containing species 74.9 75.6 63.3 72.2 +Number of species-specific orthogroups 42 15 4 35 +Number of genes in species-specific orthogroups 189 116 9 112 +Percentage of genes in species-specific orthogroups 23.0 15.2 1.9 16.6 + + +Number of genes per-species in orthogroup Number of orthogroups Number of orthogroups Number of orthogroups Number of orthogroups +'0 156 152 228 173 +'1 392 423 367 398 +'2 35 34 20 27 +'3 25 4 5 10 +'4 5 2 1 6 +'5 3 0 0 2 +'6 2 1 0 2 +'7 0 2 0 2 +'8 0 1 0 1 +'9 0 1 0 0 +'10 1 0 1 0 +11-15 2 1 0 1 +16-20 0 0 0 0 +21-50 1 0 0 0 +51-100 0 1 0 0 +101-150 0 0 0 0 +151-200 0 0 0 0 +201-500 0 0 0 0 +501-1000 0 0 0 0 +'1001+ 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups Percentage of orthogroups +'0 25.1 24.4 36.7 27.8 +'1 63.0 68.0 59.0 64.0 +'2 5.6 5.5 3.2 4.3 +'3 4.0 0.6 0.8 1.6 +'4 0.8 0.3 0.2 1.0 +'5 0.5 0.0 0.0 0.3 +'6 0.3 0.2 0.0 0.3 +'7 0.0 0.3 0.0 0.3 +'8 0.0 0.2 0.0 0.2 +'9 0.0 0.2 0.0 0.0 +'10 0.2 0.0 0.2 0.0 +11-15 0.3 0.2 0.0 0.2 +16-20 0.0 0.0 0.0 0.0 +21-50 0.2 0.0 0.0 0.0 +51-100 0.0 0.2 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 + +Number of genes per-species in orthogroup Number of genes Number of genes Number of genes Number of genes +'0 0 0 0 0 +'1 392 423 367 398 +'2 70 68 40 54 +'3 75 12 15 30 +'4 20 8 4 24 +'5 15 0 0 10 +'6 12 6 0 12 +'7 0 14 0 14 +'8 0 8 0 8 +'9 0 9 0 0 +'10 10 0 10 0 +11-15 26 13 0 12 +16-20 0 0 0 0 +21-50 39 0 0 0 +51-100 0 58 0 0 +101-150 0 0 0 0 +151-200 0 0 0 0 +201-500 0 0 0 0 +501-1000 0 0 0 0 +'1001+ 0 0 0 0 + +Number of genes per-species in orthogroup Percentage of genes Percentage of genes Percentage of genes Percentage of genes +'0 0.0 0.0 0.0 0.0 +'1 47.8 55.4 77.1 59.1 +'2 8.5 8.9 8.4 8.0 +'3 9.1 1.6 3.2 4.5 +'4 2.4 1.0 0.8 3.6 +'5 1.8 0.0 0.0 1.5 +'6 1.5 0.8 0.0 1.8 +'7 0.0 1.8 0.0 2.1 +'8 0.0 1.0 0.0 1.2 +'9 0.0 1.2 0.0 0.0 +'10 1.2 0.0 2.1 0.0 +11-15 3.2 1.7 0.0 1.8 +16-20 0.0 0.0 0.0 0.0 +21-50 4.8 0.0 0.0 0.0 +51-100 0.0 7.6 0.0 0.0 +101-150 0.0 0.0 0.0 0.0 +151-200 0.0 0.0 0.0 0.0 +201-500 0.0 0.0 0.0 0.0 +501-1000 0.0 0.0 0.0 0.0 +'1001+ 0.0 0.0 0.0 0.0 |