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Options to start from orthogroups or trees. Allow user-provided speci…
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@davidemms
davidemms committed Nov 25, 2016
1 parent 8a0ef5c commit cbacdb5
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Showing 415 changed files with 136,089 additions and 528 deletions.
2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddOneRemoveOne/Orthogroups.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243
OG0000000 gi|290752526|emb|CBH40498.1|, gi|290752801|emb|CBH40776.1|, gi|290752802|emb|CBH40777.1| 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|84626133|gb|AAC71526.2| gi|71851738|gb|AAZ44346.1|, gi|71851739|gb|AAZ44347.1|, gi|71851837|gb|AAZ44445.1|
OG0000001 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|1046010|gb|AAC71532.1|, gi|3844907|gb|AAC71551.1|, gi|3844927|gb|AAC71569.1| gi|144227478|gb|AAZ44221.2|
OG0000002 gi|290752376|emb|CBH40347.1|, gi|290752697|emb|CBH40671.1|, gi|290753074|emb|CBH41050.1| gi|3845025|gb|AAC72453.1|, gi|3845036|gb|AAC72463.1| gi|144227479|gb|AAZ44222.2|
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8 changes: 4 additions & 4 deletions Tests/ExpectedOutput/AddOneRemoveOne/Orthogroups_SpeciesOverlaps.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa
Mycoplasma_agalactiae_5632_FP671138.faa 414 303 390
Mycoplasma_genitalium_uid97_L43967.faa 303 316 292
Mycoplasma_hyopneumoniae_AE017243.faa 390 292 403
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243
Mycoplasma_agalactiae_5632_FP671138 414 303 390
Mycoplasma_genitalium_uid97_L43967 303 316 292
Mycoplasma_hyopneumoniae_AE017243 390 292 403
2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddOneRemoveOne/Orthogroups_UnassignedGenes.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243
OG0000427 gi|290752272|emb|CBH40243.1|
OG0000428 gi|290752276|emb|CBH40247.1|
OG0000429 gi|290752279|emb|CBH40250.1|
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2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddOneRemoveOne/Statistics_PerSpecies.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243
Number of genes 820 476 674
Number of genes in orthogroups 457 346 417
Number of unassigned genes 363 130 257
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2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddOneSpecies/Orthogroups.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_gallisepticum_uid409_AE015450
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|
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|
OG0000002 gi|290752526|emb|CBH40498.1|, gi|290752801|emb|CBH40776.1|, gi|290752802|emb|CBH40777.1|, gi|290753081|emb|CBH41057.1| 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|3845062|gb|AAC72487.1|, gi|3845064|gb|AAC72489.1|, gi|84626133|gb|AAC71526.2| gi|144227640|gb|AAZ44535.2|, gi|71851738|gb|AAZ44346.1|, gi|71851739|gb|AAZ44347.1|, gi|71851837|gb|AAZ44445.1| gi|31541070|gb|AAP56372.1|, gi|31541268|gb|AAP56569.1|, gi|31541628|gb|AAP56928.1|, gi|31541629|gb|AAP56929.1|
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10 changes: 5 additions & 5 deletions Tests/ExpectedOutput/AddOneSpecies/Orthogroups_SpeciesOverlaps.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138.faa 430 302 389 358
Mycoplasma_genitalium_uid97_L43967.faa 302 392 294 383
Mycoplasma_hyopneumoniae_AE017243.faa 389 294 416 344
Mycoplasma_gallisepticum_uid409_AE015450.faa 358 383 344 459
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_gallisepticum_uid409_AE015450
Mycoplasma_agalactiae_5632_FP671138 430 302 389 358
Mycoplasma_genitalium_uid97_L43967 302 392 294 383
Mycoplasma_hyopneumoniae_AE017243 389 294 416 344
Mycoplasma_gallisepticum_uid409_AE015450 358 383 344 459
2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddOneSpecies/Orthogroups_UnassignedGenes.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_gallisepticum_uid409_AE015450
OG0000536 gi|290752272|emb|CBH40243.1|
OG0000537 gi|290752276|emb|CBH40247.1|
OG0000538 gi|290752279|emb|CBH40250.1|
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2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddOneSpecies/Statistics_PerSpecies.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_gallisepticum_uid409_AE015450
Number of genes 820 476 674 763
Number of genes in orthogroups 503 429 445 561
Number of unassigned genes 317 47 229 202
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2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddTwoSpecies/Orthogroups.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_bovis.GCA_001043135.1.29.pep.all.fa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_bovis Mycoplasma_gallisepticum_uid409_AE015450
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|
OG0000001 gi|290752501|emb|CBH40473.1|, 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| AKO50922, AKO50923
OG0000002 gi|290752288|emb|CBH40259.1|, gi|290752368|emb|CBH40339.1|, 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|290752811|emb|CBH40786.1|, gi|290752820|emb|CBH40795.1|, gi|290753018|emb|CBH40994.1|, gi|290753048|emb|CBH41024.1| AKO50335, AKO50391, AKO50396, AKO50510, AKO50535, AKO50545, AKO50616, AKO50624, AKO50729, AKO50997
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12 changes: 6 additions & 6 deletions Tests/ExpectedOutput/AddTwoSpecies/Orthogroups_SpeciesOverlaps.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_bovis.GCA_001043135.1.29.pep.all.fa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138.faa 627 305 395 620 364
Mycoplasma_genitalium_uid97_L43967.faa 305 396 296 304 386
Mycoplasma_hyopneumoniae_AE017243.faa 395 296 423 394 345
Mycoplasma_bovis.GCA_001043135.1.29.pep.all.fa 620 304 394 626 362
Mycoplasma_gallisepticum_uid409_AE015450.faa 364 386 345 362 464
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_bovis Mycoplasma_gallisepticum_uid409_AE015450
Mycoplasma_agalactiae_5632_FP671138 627 305 395 620 364
Mycoplasma_genitalium_uid97_L43967 305 396 296 304 386
Mycoplasma_hyopneumoniae_AE017243 395 296 423 394 345
Mycoplasma_bovis 620 304 394 626 362
Mycoplasma_gallisepticum_uid409_AE015450 364 386 345 362 464
2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddTwoSpecies/Orthogroups_UnassignedGenes.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_bovis.GCA_001043135.1.29.pep.all.fa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_bovis Mycoplasma_gallisepticum_uid409_AE015450
OG0000736 gi|290752286|emb|CBH40257.1|
OG0000737 gi|290752287|emb|CBH40258.1|
OG0000738 gi|290752289|emb|CBH40260.1|
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2 changes: 1 addition & 1 deletion Tests/ExpectedOutput/AddTwoSpecies/Statistics_PerSpecies.csv
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Mycoplasma_agalactiae_5632_FP671138.faa Mycoplasma_genitalium_uid97_L43967.faa Mycoplasma_hyopneumoniae_AE017243.faa Mycoplasma_bovis.GCA_001043135.1.29.pep.all.fa Mycoplasma_gallisepticum_uid409_AE015450.faa
Mycoplasma_agalactiae_5632_FP671138 Mycoplasma_genitalium_uid97_L43967 Mycoplasma_hyopneumoniae_AE017243 Mycoplasma_bovis Mycoplasma_gallisepticum_uid409_AE015450
Number of genes 820 476 674 763 763
Number of genes in orthogroups 728 429 451 704 561
Number of unassigned genes 92 47 223 59 202
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