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add expected_output
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@sinamajidian
sinamajidian committed Oct 18, 2024
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167 changes: 167 additions & 0 deletions testdata/expected_output/FastOMA_HOGs.orthoxml
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<?xml version='1.0' encoding='utf-8'?>
<orthoXML xmlns="http://orthoXML.org/2011/" origin="FastOMA 0.3.4+dev" originVersion="2024-10-18 02:51:20" version="0.5">
<species name="MYCGE" taxonId="5" NCBITaxId="0">
<database name="database" version="2023">
<genes>
<gene id="1000000001" protId="sp|P47500|RF1_MYCGE" />
<gene id="1000000002" protId="sp|P13927|EFTU_MYCGE" />
<gene id="1000000003" protId="sp|P47639|ATPB_MYCGE" />
<gene id="1000000004" protId="sp|P47547|DNAK_MYCGE" />
<gene id="1000000005" protId="sp|P47543|G3P_MYCGE" />
<gene id="1000000006" protId="sp|P47641|ATPA_MYCGE" />
</genes>
</database>
</species>
<species name="CHLTR" taxonId="4" NCBITaxId="0">
<database name="database" version="2023">
<genes>
<gene id="1001000001" protId="sp|O84067|LEPA_CHLTR" />
<gene id="1001000002" protId="sp|O84026|RF1_CHLTR" />
<gene id="1001000003" protId="sp|O84591|ENO_CHLTR" />
<gene id="1001000004" protId="sp|P0CD71|EFTU_CHLTR" />
<gene id="1001000005" protId="tr|O84829|O84829_CHLTR" />
<gene id="1001000006" protId="sp|O84332|TPIS_CHLTR" />
<gene id="1001000007" protId="sp|P17821|DNAK_CHLTR" />
<gene id="1001000008" protId="sp|O84081|FOLD_CHLTR" />
<gene id="1001000009" protId="sp|P0CE13|G3P_CHLTR" />
<gene id="1001000010" protId="sp|P0C0Z7|CH60_CHLTR" />
</genes>
</database>
</species>
<species name="AQUAE" taxonId="3" NCBITaxId="0">
<database name="database" version="2023">
<genes>
<gene id="1002000001" protId="sp|O67618|LEPA_AQUAE" />
<gene id="1002000002" protId="sp|O67032|RF1_AQUAE" />
<gene id="1002000003" protId="sp|O66778|ENO_AQUAE" />
<gene id="1002000004" protId="sp|O66429|EFTU_AQUAE" />
<gene id="1002000005" protId="sp|O67547|SUCD_AQUAE" />
<gene id="1002000006" protId="sp|O66686|TPIS_AQUAE" />
<gene id="1002000007" protId="sp|O67828|ATPB_AQUAE" />
<gene id="1002000008" protId="sp|O67118|DNAK_AQUAE" />
<gene id="1002000009" protId="sp|O67736|FOLD_AQUAE" />
<gene id="1002000010" protId="sp|O67161|G3P_AQUAE" />
<gene id="1002000011" protId="sp|O67943|CH60_AQUAE" />
<gene id="1002000012" protId="sp|O66907|ATPA_AQUAE" />
</genes>
</database>
</species>
<taxonomy>
<taxon id="1" name="inter2">
<taxon id="2" name="inter1">
<taxon id="3" name="AQUAE" />
<taxon id="4" name="CHLTR" />
</taxon>
<taxon id="5" name="MYCGE" />
</taxon>
</taxonomy>
<scores>
<scoreDef id="CompletenessScore" desc="Fraction of expected species with genes in the (Sub)HOG" />
</scores>
<groups>
<orthologGroup id="HOG:0000001_1" taxonId="1">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E1027400" />
<property name="TaxRange" value="inter2" />
<geneRef id="1000000005" />
<orthologGroup id="HOG:0000001_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000010" />
<geneRef id="1001000009" />
</orthologGroup>
</orthologGroup>
<orthologGroup id="HOG:0000002_1" taxonId="1">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E0990770" />
<property name="TaxRange" value="inter2" />
<geneRef id="1000000004" />
<orthologGroup id="HOG:0000002_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000008" />
<geneRef id="1001000007" />
</orthologGroup>
</orthologGroup>
<orthologGroup id="HOG:0000003_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E0990677" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000001" />
<geneRef id="1001000001" />
</orthologGroup>
<orthologGroup id="HOG:0000004_1" taxonId="1">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E0990677" />
<property name="TaxRange" value="inter2" />
<geneRef id="1000000002" />
<orthologGroup id="HOG:0000004_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000004" />
<geneRef id="1001000004" />
</orthologGroup>
</orthologGroup>
<orthologGroup id="HOG:0000005_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E1027325" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000009" />
<geneRef id="1001000008" />
</orthologGroup>
<orthologGroup id="HOG:0000006_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E1027829" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000006" />
<geneRef id="1001000006" />
</orthologGroup>
<orthologGroup id="HOG:0000007_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E1027301" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000011" />
<geneRef id="1001000010" />
</orthologGroup>
<orthologGroup id="HOG:0000008_1" taxonId="1">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E0990823" />
<property name="TaxRange" value="inter2" />
<geneRef id="1002000007" />
<geneRef id="1000000003" />
</orthologGroup>
<orthologGroup id="HOG:0000009_1" taxonId="1">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E0990823" />
<property name="TaxRange" value="inter2" />
<geneRef id="1002000012" />
<geneRef id="1000000006" />
</orthologGroup>
<orthologGroup id="HOG:0000010_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E1027309" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000003" />
<geneRef id="1001000003" />
</orthologGroup>
<orthologGroup id="HOG:0000011_1" taxonId="1">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E0990790" />
<property name="TaxRange" value="inter2" />
<geneRef id="1000000001" />
<orthologGroup id="HOG:0000011_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000002" />
<geneRef id="1001000002" />
</orthologGroup>
</orthologGroup>
<orthologGroup id="HOG:0000012_2" taxonId="2">
<score id="CompletenessScore" value="1.0" />
<property name="OMAmerRootHOG" value="HOG:E1027626" />
<property name="TaxRange" value="inter1" />
<geneRef id="1002000005" />
<geneRef id="1001000005" />
</orthologGroup>
</groups>
</orthoXML>
29 changes: 29 additions & 0 deletions testdata/expected_output/OrthologousGroups.tsv
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Group Protein
OG_0000001 sp|P0CE13|G3P_CHLTR
OG_0000001 sp|O67161|G3P_AQUAE
OG_0000001 sp|P47543|G3P_MYCGE
OG_0000002 sp|O67118|DNAK_AQUAE
OG_0000002 sp|P47547|DNAK_MYCGE
OG_0000002 sp|P17821|DNAK_CHLTR
OG_0000003 sp|O67618|LEPA_AQUAE
OG_0000003 sp|O84067|LEPA_CHLTR
OG_0000004 sp|P0CD71|EFTU_CHLTR
OG_0000004 sp|P13927|EFTU_MYCGE
OG_0000004 sp|O66429|EFTU_AQUAE
OG_0000005 sp|O84081|FOLD_CHLTR
OG_0000005 sp|O67736|FOLD_AQUAE
OG_0000006 sp|O84332|TPIS_CHLTR
OG_0000006 sp|O66686|TPIS_AQUAE
OG_0000007 sp|P0C0Z7|CH60_CHLTR
OG_0000007 sp|O67943|CH60_AQUAE
OG_0000008 sp|P47639|ATPB_MYCGE
OG_0000008 sp|O67828|ATPB_AQUAE
OG_0000009 sp|P47641|ATPA_MYCGE
OG_0000009 sp|O66907|ATPA_AQUAE
OG_0000010 sp|O66778|ENO_AQUAE
OG_0000010 sp|O84591|ENO_CHLTR
OG_0000011 sp|O84026|RF1_CHLTR
OG_0000011 sp|O67032|RF1_AQUAE
OG_0000011 sp|P47500|RF1_MYCGE
OG_0000012 tr|O84829|O84829_CHLTR
OG_0000012 sp|O67547|SUCD_AQUAE
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>sp|P47543|G3P_MYCGE sp|P47543|G3P_MYCGE||MYCGE||1000000005 sp|P47543|G3P_MYCGE [MYCGE]
MAAKNRTIKVAINGFGRIGRLVFRSLLSKANVEVVAINDLTQPEVLAHLLKYDSAHGELK
RKITVKQNILQIDRKKVYVFSEKDPQNLPWDEHDIDVVIESTGRFVSEEGASLHLKAGAK
RVIISAPAKEKTIRTVVYNVNHKTISSDDKIISAASCTTNCLAPLVHVLEKNFGIVYGTM
LTVHAYTADQRLQDAPHNDLRRARAAAVNIVPTTTGAAKAIGLVVPEANGKLNGMSLRVP
VLTGSIVELSVVLEKSPSVEQVNQAMKRFASASFKYCEDPIVSSDVVSSEYGSIFDSKLT
NIVEVDGMKLYKVYAWYDNESSYVHQLVRVVSYCAKL
>sp|P0CE13|G3P_CHLTR sp|P0CE13|G3P_CHLTR||CHLTR||1001000009 sp|P0CE13|G3P_CHLTR [CHLTR]
MRIVINGFGRIGRLVLRQILKRNSPIEVVAINDLVAGDLLTYLFKYDSTHGSFAPQATFS
DGCLVMGERKVHFLAEKDVQKLPWKDLDVDVVVESTGLFVNRDDVAKHLDSGAKRVLITA
PAKGDVPTFVMGVNHQQFDPADVIISNASCTTNCLAPLAKVLLDNFGIEEGLMTTVHAAT
ATQSVVDGPSRKDWRGGRGAFQNIIPASTGAAKAVGLCLPELKGKLTGMAFRVPVADVSV
VDLTVKLSSATTYEAICEAVKHAANTSMKNIMYYTEEAVVSSDFIGCEYSSVFDAQAGVA
LNDRFFKLVAWYDNEIGYATRIVDLLEYVQENSK
>sp|O67161|G3P_AQUAE sp|O67161|G3P_AQUAE||AQUAE||1002000010 sp|O67161|G3P_AQUAE [AQUAE]
MAIKVGINGFGRIGRSFFRASWGREEIEIVAINDLTDAKHLAHLLKYDSVHGIFKGSVEA
KDDSIVVDGKEIKVFAQKDPSQIPWGDLGVDVVIEATGVFRDRENASKHLQGGAKKVIIT
APAKNPDITVVLGVNEEKYNPKEHNIISNASCTTNCLAPCVKVLNEAFGVEKGYMVTVHA
YTNDQRLLDLPHKDFRRARAAAINIVPTTTGAAKAIGEVIPELKGKLDGTARRVPVPDGS
LIDLTVVVNKAPSSVEEVNEKFREAAQKYRESGKVYLKEILQYCEDPIVSTDIVGNPHSA
IFDAPLTQVIDNLVHIAAWYDNEWGYSCRLRDLVIYLAERGL
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29 changes: 29 additions & 0 deletions testdata/expected_output/RootHOGs.tsv
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RootHOG Protein OMAmerRootHOG
HOG:0000001 sp|P0CE13|G3P_CHLTR HOG:E1027400
HOG:0000001 sp|O67161|G3P_AQUAE HOG:E1027400
HOG:0000001 sp|P47543|G3P_MYCGE HOG:E1027400
HOG:0000002 sp|O67118|DNAK_AQUAE HOG:E0990770
HOG:0000002 sp|P47547|DNAK_MYCGE HOG:E0990770
HOG:0000002 sp|P17821|DNAK_CHLTR HOG:E0990770
HOG:0000003 sp|O67618|LEPA_AQUAE HOG:E0990677
HOG:0000003 sp|O84067|LEPA_CHLTR HOG:E0990677
HOG:0000004 sp|P0CD71|EFTU_CHLTR HOG:E0990677
HOG:0000004 sp|P13927|EFTU_MYCGE HOG:E0990677
HOG:0000004 sp|O66429|EFTU_AQUAE HOG:E0990677
HOG:0000005 sp|O84081|FOLD_CHLTR HOG:E1027325
HOG:0000005 sp|O67736|FOLD_AQUAE HOG:E1027325
HOG:0000006 sp|O84332|TPIS_CHLTR HOG:E1027829
HOG:0000006 sp|O66686|TPIS_AQUAE HOG:E1027829
HOG:0000007 sp|P0C0Z7|CH60_CHLTR HOG:E1027301
HOG:0000007 sp|O67943|CH60_AQUAE HOG:E1027301
HOG:0000008 sp|P47639|ATPB_MYCGE HOG:E0990823
HOG:0000008 sp|O67828|ATPB_AQUAE HOG:E0990823
HOG:0000009 sp|P47641|ATPA_MYCGE HOG:E0990823
HOG:0000009 sp|O66907|ATPA_AQUAE HOG:E0990823
HOG:0000010 sp|O66778|ENO_AQUAE HOG:E1027309
HOG:0000010 sp|O84591|ENO_CHLTR HOG:E1027309
HOG:0000011 sp|O84026|RF1_CHLTR HOG:E0990790
HOG:0000011 sp|O67032|RF1_AQUAE HOG:E0990790
HOG:0000011 sp|P47500|RF1_MYCGE HOG:E0990790
HOG:0000012 tr|O84829|O84829_CHLTR HOG:E1027626
HOG:0000012 sp|O67547|SUCD_AQUAE HOG:E1027626
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>sp|P47543|G3P_MYCGE sp|P47543|G3P_MYCGE||MYCGE||1000000005 sp|P47543|G3P_MYCGE [MYCGE]
MAAKNRTIKVAINGFGRIGRLVFRSLLSKANVEVVAINDLTQPEVLAHLLKYDSAHGELK
RKITVKQNILQIDRKKVYVFSEKDPQNLPWDEHDIDVVIESTGRFVSEEGASLHLKAGAK
RVIISAPAKEKTIRTVVYNVNHKTISSDDKIISAASCTTNCLAPLVHVLEKNFGIVYGTM
LTVHAYTADQRLQDAPHNDLRRARAAAVNIVPTTTGAAKAIGLVVPEANGKLNGMSLRVP
VLTGSIVELSVVLEKSPSVEQVNQAMKRFASASFKYCEDPIVSSDVVSSEYGSIFDSKLT
NIVEVDGMKLYKVYAWYDNESSYVHQLVRVVSYCAKL
>sp|P0CE13|G3P_CHLTR sp|P0CE13|G3P_CHLTR||CHLTR||1001000009 sp|P0CE13|G3P_CHLTR [CHLTR]
MRIVINGFGRIGRLVLRQILKRNSPIEVVAINDLVAGDLLTYLFKYDSTHGSFAPQATFS
DGCLVMGERKVHFLAEKDVQKLPWKDLDVDVVVESTGLFVNRDDVAKHLDSGAKRVLITA
PAKGDVPTFVMGVNHQQFDPADVIISNASCTTNCLAPLAKVLLDNFGIEEGLMTTVHAAT
ATQSVVDGPSRKDWRGGRGAFQNIIPASTGAAKAVGLCLPELKGKLTGMAFRVPVADVSV
VDLTVKLSSATTYEAICEAVKHAANTSMKNIMYYTEEAVVSSDFIGCEYSSVFDAQAGVA
LNDRFFKLVAWYDNEIGYATRIVDLLEYVQENSK
>sp|O67161|G3P_AQUAE sp|O67161|G3P_AQUAE||AQUAE||1002000010 sp|O67161|G3P_AQUAE [AQUAE]
MAIKVGINGFGRIGRSFFRASWGREEIEIVAINDLTDAKHLAHLLKYDSVHGIFKGSVEA
KDDSIVVDGKEIKVFAQKDPSQIPWGDLGVDVVIEATGVFRDRENASKHLQGGAKKVIIT
APAKNPDITVVLGVNEEKYNPKEHNIISNASCTTNCLAPCVKVLNEAFGVEKGYMVTVHA
YTNDQRLLDLPHKDFRRARAAAINIVPTTTGAAKAIGEVIPELKGKLDGTARRVPVPDGS
LIDLTVVVNKAPSSVEEVNEKFREAAQKYRESGKVYLKEILQYCEDPIVSTDIVGNPHSA
IFDAPLTQVIDNLVHIAAWYDNEWGYSCRLRDLVIYLAERGL
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