Merge pull request #11 from JLSteenwyk/new_python_and_biopython_versions

New python and biopython versions

docs/usage/index.rst

@@ -87,7 +87,7 @@ To report inparalogs and specify which was kept per SNAP-OG, use the -rih, \-\-r
 argument. The resulting file, which will have the suffix ".inparalog_report.txt," will have three columns: |br|
 - col 1 is the orthogroup file |br|
 - col 2 is the inparalog that was kept |br|
-- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";" |br|
+- col 3 is/are the inparalog/s that were trimmed separated by a semi-colon ";"
 
 To generate this file, use the following command:
 
@@ -125,3 +125,8 @@ All options
 +-------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
 *For genome-scale analyses, we recommend changing the -o/\-\-occupancy parameter to be the same for all large gene families so that the minimum SNAP-OG occupancy is the same
 for all SNAP-OGs.
+
+
+.. |br| raw:: html
+
+  <br/>

orthosnap/helper.py

@@ -375,7 +375,6 @@ def write_output_fasta_and_account_for_assigned_tips_single_copy_case(
     write_summary_file_with_inparalog_handling(
         inparalog_handling, fasta,
         output_path, subgroup_counter,
-        assigned_tips
     )
     subgroup_counter += 1
 
@@ -387,7 +386,6 @@ def write_summary_file_with_inparalog_handling(
         fasta: str,
         output_path: str,
         subgroup_count: int,
-        assigned_tips: list
 ):
     res_arr = []
 
@@ -406,10 +404,19 @@ def write_summary_file_with_inparalog_handling(
         f"{output_path}/{fasta_path_stripped}.orthosnap.{subgroup_count}.fa"
     )
 
-    if res_arr:
+    for i in res_arr:
         try:
-            if res_arr[0][1] in open(output_fasta_file_name).read():
+            if string_exact_match(f">{i[1]}", output_fasta_file_name):
                 with open(f"{output_path}{inparalog_report_output_name}", "a") as file:
-                    file.writelines('\t'.join(i) + '\n' for i in res_arr)
+                    file.writelines('\t'.join(i) + '\n')
         except FileNotFoundError:
             1
+
+
+def string_exact_match(string, filename):
+    with open(filename, 'r') as f:
+        for line in f:
+            line = line.rstrip()
+            if re.search(r'\b{}\b'.format(string), line):
+                return True
+    return False

orthosnap/orthosnap.py

@@ -150,7 +150,6 @@ def execute(
             fasta,
             output_path,
             subgroup_counter,
-            assigned_tips,
         )
 
     write_output_stats(

orthosnap/version.py

@@ -1 +1 @@
-__version__ = "1.2.0"
+__version__ = "1.3.0"

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.inparalog_report.txt

@@ -0,0 +1,3 @@
+fake_orthologous_group_of_genes.faa.orthosnap.0	species0|gene0-duplicate_copy_1	species0|gene0-duplicate_copy_2;species0|gene0-duplicate_copy_0
+fake_orthologous_group_of_genes.faa.orthosnap.1	species4|gene2-duplicate_copy_1	species4|gene2-duplicate_copy_0
+fake_orthologous_group_of_genes.faa.orthosnap.1	species2|gene2-duplicate_copy_1	species2|gene2-duplicate_copy_0

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.0.fa

@@ -0,0 +1,14 @@
+>species0|gene0-duplicate_copy_1
+MFGAVAAGSEESPQAPRCISTRSSSFRVYLSAWNFGMSPERVTTEPLHSPDWDNDWLRQL
+AGDIVAGSLSATIIAPITTVIDRSVVERLSSNRSILHTLRTHAICSILKPRKFYFSRPFF
+IAWSLYAATYATANATDTSLEHLSKVTEKSTTASLVPTFSFLPTYVVNVCLGILKDIRFS
+QIYGHPEGRLKQPPPIPRLAYMAFLFRDSITISSSFTLAPQVASLVPDWITADPHTKRTV
+TQLALPALVQYVNTPFHMIALDVIARPQVATIAERSVTIRRGDLAEILNSPAYDYGQDVE
+KKKNLDDTSPEDEDPFGNEEFAEVKYRTMGWWKTGILMVAENVSIGILSLPSAFATLGFV
+PALIILIGISGISWYTAYILCQFKLRYPQVHSMGDAGEIIMGRFGRELLGIGQLLFLIFV
+MASHVLTFTVLMNTITEHGTCTIVFGVIALIVSCVGALPRTMDKVYWMSIASFLSIVAAT
+MATMIAVGVEYKGHIPLAVTTHLSFNEEFLAVSNLFFAYVGHASFFGFISEMDKPREFTK
+SISVLQVIDTSLYIASAVVIYRYVGADVQSPALGSAGPLGKKIAYGLAIPTVLIAGIVNG
+HVASKYVYVRVFRGTNHMHERTLLSIGSWVAIGLISWVVAWVIAESIPVFNNLLSLITAL
+FGCWFAYGFPAIFWFTLNKGQWFASSRKIFLTLSNTFILAMAITLCGLGLYVSGDAISKD
+SGSGVWTCANNAVTTTTTT

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.1.fa

@@ -0,0 +1,45 @@
+>species4|gene2-duplicate_copy_1
+MAVSRDLEAPAVVNDPTADDAMVEKKEYADGTPANDPFGNEECGEVRYRVMSWWQCGTLM
+VAENISLGILSLPSAVATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGE
+LLMGRFGRELFGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGAL
+PRTMGKVYWMSMASCISIVTATVVTMIAIGVQAPDHVHVDATTEVSFQDAFLAVTNIIFA
+YIAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGP
+LMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALGVWV
+VAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFLI
+LAFACALCGMGLYVSGKSIHDSSSKASWTCKNNATTTT
+>species2|gene2-duplicate_copy_1
+MMLWLKRRNMLMGRRQMTRLEMKNAERSNIVSCRGVMVAENISLGILSLSSAVATLGIVP
+AVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGELLMGRFGRELFGIGQLLFLIFLM
+ASHILTFSVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWMSMASCISIVTATV
+VTMIAIGVQAPDHVHVNVTTKVSFQDAFLAVTNIIFAYIAHVAFFGFISEMHDPRDFPKS
+LTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGPLMKKVAYGLAIPTVVIAGVVFGH
+VACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALGVWVVAWVIAESIPVFNELLSLISSLF
+GSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFFILAFACALCGMGLYVSGKSIHDSS
+SKASWTCKNNAT
+>species1|gene2
+MAVSRDLEAPAVVNDPTAYDATVEKKEYADGTPANDPFGNEECGEVKYRVMSWWQCGTLM
+VAENISLGILSLPSAVATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQVHSMGDAGE
+LLMGRFGRELFGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGAL
+PRTMGKVYWMSMASCISIVTATVVTMIAIGVQAPEHVHVDATTEVSFQDAFLAVTNIIFA
+YIAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGP
+VMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALSVWV
+VAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFLI
+LAFACALCGMGLYVSGKSIHDSSSKASWTCKNNAT
+>species3|gene7
+MAPTTRDLEALTVHHDSDIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCG
+ILMIAENISLGILSLPSAVATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGD
+AGEILFGRIGREILFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFI
+GALPRTMGKVYWMSLASCTSITVATIVTMVAIAMQAPDHVQVDITTHPSFSTAFLSVTNI
+VFAFIAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASPALSS
+AGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWRGSPQMHTNSLAAVGSWVAIALG
+VWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIFLTIVN
+LVIFGIACAICGLGLYVSGKAIHDSSSSASWTCANNAST
+>species0|gene1
+MAPTTRDLEALAVHHDSDIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCG
+ILMIAENISLGILSLPSAVATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGD
+AGEILFGRIGREILFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFI
+GALPRTMGKVYWMSLASCTSITVATIVTMVAIAVQAPDHVQVDITTHPSFSTAFLSVTNI
+VFAFIAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASPALSS
+AGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWRGSPQMHTNSLAAVGSWVAIALG
+VWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIFLTIVN
+LVIFGIACAICGLGLYVSGKAIHDSSSSASWTCANNAST

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.2.fa

@@ -0,0 +1,44 @@
+>species2|gene5
+MSPDTSDLDLETRPAVSLNRGEEYKEQPETPDEEPFGDEDDAEVRYRTLEWWFVSPVMLA
+GGTSLGILTLPSAVATLGIVPGVILIVGIAILTVYTGYVMGQFKQRYPHVHSIADGGEVL
+FGWVGREILGAGLLLCLVFVMGGHILTFTVMMNTLTDHGTCSVVFGVVGLLISLILSLPR
+TFKRMSWLSVISFASIVGAVLVTMIALGVQRPPNVRVEVTRPTSLYRAFLAVTDIVFAYA
+AHPAFFGFISEMKTPTDWPKTLCFVEIINTTLYTVTGVVIYRFAGQHVASPALGSTSPLM
+AKVAYGTAIPTIVIAGVINGHIACKYIYVRVFRGTEHMHRRSLFAIGTWVVISVVLWTVA
+WVIAEAVPEFNNLLSLITSLFCSWFSYGLCGAFWLFINKGLWFSSPRKTFLTIVNFTLLG
+MGACLCGLGLYASGRAISEESAGRIFSCASTA
+>species4|gene1
+MSPDTSDLDLETRPAVSLNRGEGYKEQPETPDEEPFGNEEGAEVRYRTLEWWFVSPGSAE
+GRQSRSDVACEQEMRDSHAGWGHIARHPNASLGCGDTGNRPVGLPGVILIVGIAILTVYT
+GCVMGQFKQRYPHVHSIADGGEVLFGWIGREVLGAGLLLCLVFVMGGHILTFTVMMNTLT
+DHGTCSVVFGVVGLLISLILSLPRTFKRMSWLSVISFASIVAAVLVTMIALGVQRPPNVK
+VEVTRPTSLYRAFLAVTDIVFAYAAHPAFFGYISEMKTPTDWPKTLCFVEVINTTLYTVT
+GVVIYRFAGQHVASPALGSSSPLMAKVAYGIAIPTIVIAGVINGHIACKYIYVRLFRGTE
+RMHQRSLFSIGTWVAISVVLWTIAWVIAEAVPEFNNLLSLITSLFCSWFSYGLCGAFWLF
+INQGLWFSSPRKTFLTIVNFTLLGMGACLCGLGLYASGRAISEESAGRSFSCASTA
+>species1|gene0
+MSPDTSDLDLGTRPAVSLNRGEGYKEQPETPDEEPFGDEEGAEVRYRTLEWWFVSPGSAE
+GRQSRSDVACEQEMRDRGVILIVGIAILTVYTGCVMGQFKQRYPHVHSIADGGEVLFGWI
+GREVLGTGLLLCLVFVMGGHILTFTVMMNTLTDHGTCSIVFGVVGLLISLILSLPRTFKR
+MSWLSVISFASIVAAVLVTMIALGVQRPPNVKVEVTRPTSLYRAFLAVTDIVFAYAAHPA
+FFGYISEMKTPTDWPKTLCFVEVINTTLYTVTGVVIYRFAGQHVASPALGSSSPLMAKVA
+YGIAIPTIVIAGVINGHIACKYIYVRLFRGTEHMHQRSLFAIGTWVAISVVLWTIAWVIA
+EAVPEFNNLLSLVLVFVCVSF
+>species3|gene3
+MSPPSAINNPGDPLAEQEKPVGARNTTGTEDPFSHDGVGGVKYRTLAWWQCAMIMVAETI
+SLGILSLPSAVASLGLVAAVILILGLGALATYTGYTLGQFKLRYPHVHSMGDAGEVLMGR
+IGREVLGTAQLLFLIFIMGSHLLTFTVMMNTLTDHGTCSIVFGVIGLAVSFAFTLPRTLK
+KVSWFSISSFISIIAAVLITMIAIAIQKPGGGRVDAIVDNSFYKAFLAVTNIVFAYAGHV
+AFFGFISEMRTPTDYPKTLYMLQGIDTSMYTISAVVIYRYGGRDVASPALGSTSPLMSKI
+AYGIAIPTIVIAGVINGHVACKYIYVRLFRGTDRMHQRGLVSIGTWVMIGLVLWTLAWII
+AEAIPVFNDLLSLITALFASWFTYGLSGIFWLFLNWGRYSSSRRKILLTGLNLLVVVVGG
+CLCALGLYVSGKSIHDHPRSSSFSCANNA
+>species0|gene8
+MSPPSAINNPGDPLAEQEKPAGARNTTGTEDPFSHDGVGGVKYRTLAWWQCAMIMVAETI
+SLGILSLPSAVASLGLVAAVILIIGLGALATYTGYTLGQFKLRYPHVHSMGDAGEVLMGR
+IGREVLGTAQLLFLIFIMGSHLLTFTVMMNTLTDHGTCSIVFGVIGLAVSFAFTLPRTLK
+KVSWFSISSFISIIAAVLITMIAIAIQKPGGGRVDAIVDNSFYKAFLAVTNIVFAYAGHV
+AFFGFISEMRTPTDYPKTLYMLQGIDTSMYTISAVVIYRYGGRDVASPALGSTSPLMSKI
+AYGIAIPTIVIAGVINGHVACKYIYVRLFRGTDRMHQRGLVSIGTWVIIGLVLWTLAWII
+AEAIPVFNDLLSLITALFASWFTYGLSGIFWLFLNWGRYSSSRRKILLTGLNLLVVVVGG
+CLCALGLYVSGKSIHDHPRSSSFSCANNA

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.3.fa

@@ -0,0 +1,18 @@
+>species3|gene4
+MSTLDVKDIENGPARRVEEEGGMWENDMEKTPSVERDPFGNEAVGEVHYKTLDWWQSGML
+MIAETVSLGVLSLPATVAEVGLIPAIILIVGMGIIATYSGYVIGQFRARYPFIHSMADAG
+EVLCGRYGRMFTEFAQLVFFMFASGXHLVTFTVMMNTLTNHGTCSVVFGVVGLVLSFACS
+LPRTMKNVSWLAVTSFLSIFTAVLITMIGVAVEHPNPPPMQLTRSTSFVKGFSAVTNIAF
+AYCGHPAFFGFIAEMKEPKDFPKSLCMLQGFEIVFYTVASAVIYRYAGQNVTSPALGSAG
+IVVRKVAYGIAIPTIVIAGVVLGHVAIKNVYVRLFRGTDVMHKRSALGIGAWIGLAAGYW
+IIAWVIAEAIPVFSDLVSLVSALFASWFSFGLPGVFWLYMYWGNYFTSVRKTLLTLANLA
+LFGIGATICVCGLWVSGLSISSDSSGSSFSCANNA
+>species0|gene7
+MSTLDVKDIENGPARRVEEEGGMWENDMEKTPSVERDPFGNEAVGEVHYKTLDWWQSGML
+MIAETVSLGVLSLPATVAEVGLIPAIILIVGMGIIATYSGYVIGQFRARYPFIHSMADAG
+EVLCGRYGRMFTEFAQLVFFMFASGSHLVTFTVMMNTLTNHGTCSVVFGVVGLVLSFACS
+LPRTMKNVSWLAVTSFLSIFTAVLITMIGVAVEHPNPPPMQLTRSTSFVKGFSAVTNIAF
+AYCGHPAFFGFIAEMKEPKDFPKSLCMLQGFEIVFYTVASAVIYRYAGQNVTSPALGSAG
+IIVRKVAYGIAIPTIVIAGVVLGHVAIKNVYVRLFRGTDVMHKRSALGIGAWIGLAAGYW
+IIAWVIAEAIPVFSDLVSLVSALFASWFSFGLPGVFWLYMYWGNYFTSVRKTLLTLANLA
+LFGIGATICVCGLWVSGLSISSDSSGSSFSCANNA

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.4.fa

@@ -0,0 +1,27 @@
+>species2|gene4
+MEAINANPPPYRTEKVEETKYTSDYEEEGQLKTGQVADAFGNEESAEIKYKTLKWWQCGL
+LMICESVSLGVLSLPAAVATLGLVPAVILIVGLGLLATYTGYNIGLFRERYPRIQNLGDA
+GEILMGPIGREIFGLGQFLFFIFVMGSHILTFRVMMNTVTEHGTCSIVFSVVGMVISMVL
+SIPRTMKGLTWISFASFLSIFGAVMITMISVGVQDHPGRIIEATVDTTLYSGFQAVSNIV
+FAYCAHVAFFGLIAEMENPRDFKKSLFMLQSFEISLYLTAAVVIYYFVGKDVASPALISA
+GPVMKKVAFGIAIPTIVGAGVVNGHVGLKYIYFRLCHKSDLIHRRSKRSVGIWIGLGLTC
+WVVAWIIAEAIPVFSDLNGLISALFASWFSYGLSGIYWLHLNYGQWFASPRKILLTILNI
+SIALFGLALCVLGLYASGTAIHNDTSSSSFSCANTDA
+>species4|gene0
+MEAIKANPPAYRTEKVEETKYTSDYEEEGQLKTGQVADAFGNEESAEIKYKTLKWWQCGL
+LMICESVSLGVLSLPAAVATLGLVPAVILIVGLGLLATYTGYNIGLFRERYPKIQNLGDA
+GEILMGPIGREIFGLGQFLFFIFVMGSHILTFRVMMNTITEHGTCSIVFSVVGMVISMVL
+SIPRTMKGLTWISFASFLSIFGAVMITMISVGVQDHPDRIIEATVDTTLYSGFQAVSNIV
+FAYCAHVAFFGLIAEMENPRDFKKSLFMLQSFEISLYLTAAVVIYYFVGKDVASPALISA
+GPVMKKVAFGIAIPTIVGAGVVNGHVGLKYIYFRLCHKSDLIHSRSKRSVGIWIGLGLTC
+WVVAWVIAEAIPVFSDLNGLISALFASWFSYGLSGIYWLHLNYGQWFASPRKILLTILNI
+SIALFGLALCVLGLYASGTAIHNDTSSSSFSCANTDA
+>species1|gene4
+MEAINANPPAYRTEKVEETKYTSDYEEEGQLKTGQVADAFGNEESAEIKYKTLKWWQCGL
+LMICESVSLGVLSLPAAVATLGLVPAVILIVGLGLLATYTGYNIGLFRERYPKIQNLGDA
+GEILMGPIGREIFGLGQFLFFIFVMGSHILTFRVMMNTITEHGTCSIVFSVVGMVISMVL
+SIPRTMKGLTWISFASFLSIFGAVMITMISVGVQDHPHRIIEATVDTTLYSGFQAVSNIV
+FAYCAHVAFFGLIAEMENPRDFKKSLFMLQSFEICLYLTAAVVIYYFVGKDVASPALISA
+GPVMKKVAFGIAIPTIVGAGVVNGHVGLKYIYFRLCHKSDLIHSRSKRSVGIWIGLGLTC
+WVVAWVIAEAIPVFSDLNGLISALFASWFSYGLSGIYWLHLNYGHWFASPRKILLTILNI
+SIALFGLALCVLGLYASGTAIHNDTSSSSFSCANTDA

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.5.fa

@@ -0,0 +1,28 @@
+>species3|gene0
+MQDYLDYLYPLIPIVHRPSFQQSLQQDRDREDSGFLGLVTAIAAVVIATMPSRFHFYRSA
+TPPLRFTSRRDMVRHCYDKILRLRDSTYFDHINFQKFAISYLLYAAFRQLGDHNWSRMLD
+VEATQIARLLNLHRISEYDGLNCIETQLRKKGFWLIFYGFVHNQLQNVLGERLSYLDPIL
+LHSINPEDLMPLEVDDEMIFENEVLMPPSHTPCLVTGFILHSRVFWAAIRSTCPESPAEP
+CPCVRARDAAVQVAYIQDRLHSLRFLLEDIPPLLRPWQPPDSQAIAHEGGSTGVTEMTQS
+HFASMRANLHVTHLWLQSLLVDQLEAAQAHKSEPSLVSTNHVQPMVDAKALWLQREGLCR
+QLFCILYSLPQINLEANGLHLAYKVRDIAAGLLVCPFHAAGPEAERATEYLRQSTDILSR
+LDSSEGMVTMHLQTWIDTDRIKSS
+>species0|gene5
+MEAVHDSPPPYATEGIDEKKEDISQVEQNLKPGLEESDAFGNEEFAEIKYKTLKWWQCGL
+LMICESVSLGVLSLPAAVATLGFVPAVILIVGLGILATYTGYNIGLFRERYPHIQNLADA
+GEILMGPFGRELFGLGQFLFCIFVMGSHLLTFRVMMNTITDHGTCSIVFSVVGMIISMVL
+SIPRTMKGMTWISFASFLSIFSAVMITMIGVGVEKHPGRIIEATVDTTLYTAFTAVSNIV
+FAYCAHVAFFGLIAEMEKPKDFKKSLFMLQAFEISLYVTAACVIYYYVGKDVQSPALSSA
+GPLLKKVAYGIAIPTIVGAGVVNGHIGLKYIYFRTCSKSGLIHSRSRRSVAVWIALGLAC
+WLVAWIIAEAIPVFSDLNSLISALFASWFSYGLSGIYWLHLNYGQWFASPRKIALTVLNA
+AIAVFGLVLCVLGLYASGTAIHNDANSNKIGWPIECWHNREPFRVRHSVRFLLPQALKHT
+GKYRAIRTNCWQPAICNHPESFPFGHRLRPNVAMHTRAELATQACDICRKRKVKCNVTSS
+STDVPSRCGRCARLDLPCTFLSPSRTRGPKKRSRTGSPAQEQPDWGTGGSRASGAVNYPT
+DDVCDRRMFSCIMQDYLDYLYPLIPIVHRPSFQQSLQEDRDREDSGFLGLVTAIAAVVIA
+TMPSRFHFYRSATPPLRFTSRRDMVRHCYDKILRLRDSTYFDHINFQKFAISYLLYAAFR
+QLGDHNWSRMLDVEATQIARLLNLHRISEYDGLNCIETQLRKKGFWLIFYGFVHNQLQNV
+LGERLSYLDPILLHSINPEDLMPLEVDDEMIFENEVLMPPSHTPCLVTGFILHSRVFWAA
+IRSTCPESPAEPCPCVRARDAAVQVAYIQDRLHSLRFLLEDIPPLLRPWQPPDSQAIAHE
+GGSTGVTEMTQSHFASMRANLHVTHLWLQSLLVDQLEAAQAHKSEPSLVSTNHVQPMVDA
+KALWLQREGLCRQLFCILYSLPQINLEANGLHLAYKVRDIAAGLLVCPFHPAGPEAERAT
+EYLRQSTDILSRLDSSEGMVTMHLQTWIDTDRIKSS

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.6.fa

@@ -0,0 +1,50 @@
+>species4|gene4
+MMLEGIPPPPEPIEAKQNDQEKALDDGADLKPIDNTPYIDPFGDEQNAEVKYKTLKWWQC
+GMFMIAESVSLGVLSLPATLAALGLVPAIILIVGLGILALYTGYTIGQFRQCYPHIHNLA
+DAGEILMGRFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVGMLICM
+VLSLPRTIKNLTYISFASFLSIFSAVMITMIGVAVQFKGGSNISITAETNLYHAFTGVTN
+IVFAYCAHVAFFGLIAEMEDPKEFPKSLCMLQFFEIALYVTAAIVIYYYVGNDVVSPALG
+SAGPLLKKVAYGIAIPTIVGAGVVNGHVGLKYIYVRIFRKTGRMHKRDLVSVGSWIAIGL
+SCWIIAWIIAEGIPSFTNIVSLISSLFASWFSYGLPGVYWLHINWGRWFSSPRKICLTII
+NLLVVGIGATMCGLGLYVSGKAIHDDSSNTSFTCANTAN
+>species2|gene6
+MMLDGVPQPPEPIEAKQNDQEKALDDGADLKPIDNTPYIDPFGDEQNAEVKYKTLKWWTC
+AGNVECVSYGMGKRSSRLMIAESVSLGVLSLPATLASLGLVPAIILIVGLGILALYTGYT
+IGQFRQCYPHIHNLADAGEILMGRFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHG
+TCSIVFSIVGMLICMVLSLPRTIKNLTYISFASFLSIFSAVMITMIGVAVQFKGGSNISV
+TAETNLYHAFTGVTNIVFAYCAHVAFFGLIAEMEDPKEFPKALCMLQFFEIALYVTAAIV
+IYYYVGNDVVSPALGSAGPLLKKVAYGIAIPTIVGAGVVNGHVGLKYIYVRIFRKTNRMH
+KRDLVSVGSWIAIGLSCWIIAWIIAEGIPSFTNIVSLISSLFASWFSYGLPGVYWLHINW
+GRWFSSPRKICLTIVNLLIVCIGATMCGLGLYVSGKAIHDDSSNTSFTCANTAS
+>species1|gene1
+MMLEGVPPPSEPIEAKQKDQEKALDDGADLKPIDNTPYVDPFGDEQNAEVKYKTLKWWQC
+GMFMIAESVSLGVLSLPATLAALGLVPAIILIVGLGILALYTGYTIGQFRQCYPHIHNLA
+DAGEILMGRFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVGMLICM
+VLSLPRTIKNLTYISFASFLSIFSAVMITMIGVAVQFKGGANISITTETNLYHAFTGVTN
+IVFAYCAHVAFFGLIAEMEDPKEFPKSLCMLQFFEIALYVTAAIVIYYYVGNDVVSPALG
+SAGPLLKKVAYGIAIPTIVGAGVVNGHVGLKYIYVRIFRKTGRMHKRDLVSVGSWIAIGL
+SCWIIAWIIAEGIPSFTNIVSLISSLFASWFSYGLPGVYWLHINWGRWFSSPRKICLTII
+NLLIVCIGATMCGLGLYVSGKAIHDDSSNTSFTCANTAN
+>species3|gene8
+MRLDGVAPPPDAVEPKSQREKDEDVEDLKAINNAPEVDAFGDEANAEVKYKTLKWWQCGM
+FMIAESVSLGVLSLPATMTALGLVPSLILIIGLGILALYTGYVIGQFRERHPYIHNLADA
+GEILMGSFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVAFVICLVL
+SLPRTIKNLTYISTASFLSIFSAVMITMIGVGVQYKGGQNISITTETNLYTAFSGVTQIM
+FAYCAHVAFFGLIAEMEEPKDFPKALCLLQGFEISLYVTAAIVIYYYVGNGVDSPALGSA
+GPVLKKVAYGMAIPTIIGAGVVNGHVGLKYIYVRIFRKSGRMHKNDWVSVGSWIGIGVTC
+WVIAWIIGEGIPSFSNLVSLISSLFASWFSFGLPGAYWLHMNYGQWWSSPRKCALTIINM
+LIFAIGGAMCGLGLYASGKAIHDDSSRSSFSCANNA
+>species0|gene4
+MRLLNKVALVTGSSSGIGRAIALRYAREGAKVACADITPTARSPVPNELDITTHDAISQE
+GGQAFFLQTDVGDASQMENAVLKTAQQFGRLDIMVNNAGVSLESRTPARIHETTNELYDT
+TMRINTRSVFLGSKYAITQMLKQDPHPSGDRGWIINLSSILGIVAATENPSYCASKGAVS
+NLTRQVALDYARDRIHANAICPGYTRTAIYEETTEYMHAAADLIRRHPFNGPGLPDDIAR
+VAVVLASEDASWMTGAVVPVDGGYTARFSFASIGTLVAVTTAALLRPSICNQTALSFPVT
+MRLDGVAPPPDAVEPKSQREKDEDVEDLKAIDNAPEVDAFGDEANAEVKYKTLKWWQCGM
+FMIAESVSLGVLSLPATMTALGLVPSLILIIGLGILALYTGYVIGQFRERHPYIHNLADA
+GEILMGSFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVAFVICLVL
+SLPRTIKNLTYISTASFLSIFSAVMITMIGVGVQYKGGQNISITTETNLYTAFSGVTQIM
+FAYCAHVAFFGLIAEMEEPKDFPKALCLLQGFEISLYVTAAIVIYYYVGNGVDSPALGSA
+GPVLKKVAYGMAIPTIIGAGVVNGHVGLKYIYVRIFRKSGRMHKNDWVSVGSWIGIGVTC
+WVIAWIIGEGIPSFSNLVSLISSLFASWFSFGLPGAYWLHMNYGQWWSSPRKCALTIINM
+LIFAIGGAMCGLGLYASGKAIHDDSSRSSFSCANNA

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.7.fa

@@ -0,0 +1,18 @@
+>species4|gene6
+MNAESQTQPQKPEDMDQKKEESMPPVRQDAFGDEEFAEVKYKVLKWWQGGLLMVAETISL
+GILSLPAAVGTVGLAPGLAILISMGILASYNGYVIGQIKLRIPHISSMSDAGEVLLGPFG
+RELLNAAQILLLIFIMASHILTFTVAFNVITGHATCSIVFGIVGAVISCLLSLPRTLEKV
+SWLSLVSFVSIFVAVMVTMVSIGIIKPTSTWAVAKNTDLVTGFGGVTNMVFAYASHNSFF
+TFIAELRDPREFPKALALLQSIDISLYIIAAVVIYYFAGDGVASPALGSAGPLISKIAYG
+IALPTIIIAGVINGHIAAKAIYLRMFSGTDRIHKRDWVAVGSWIGIMAVLWTISWIIAEA
+IPVFNDLIGLIAALFLSWFTFGLPGVFWLYMNKGMWFLSRRKIFLTVVNVSSVCIGLVVC
+ALGLYASGVSIHQNPAGSVFSCGARS
+>species2|gene1
+MKAESQTQAQKPEDMDQKKEEPMPPVRQDAFGDEEFAEVKYKVLKWWQGGLLMVAETISL
+GILSLPAAVGTVGLAPGLAILISMGILASYNGYVIGQIKLRFPHITSMSDAGEVLLGPFG
+RELLNAAQILLLIFIMASHILTFTVAFNVMTGHATCSIVFGVVGAVISCLLSLPRTLEKV
+SWLSLVSFVSIFAAVMVTMVSIGIIKPTSTWAVAKHTDLVTAFGGVTNMVFAYASHNSFF
+TFIAELRDPREFPKALALLQSIDISLYVVAAVVIYYFAGDGVTSPALGSAGPLISKAAYG
+IALPTIVIAGVINGHIAAKAIYLRMFSGTDRIHKRDWIAVGSWIGIMAVLWTISWIIAEA
+IPVFNDLIGLIAALFLSWFTFGLPGVFWLYMNKGIWFLSRRKLFLTVVNVASVCIGLVVV
+SIYILGSPTVLGLIDQCALGLYASGVSINHNPAGSVFSCGARS

tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.8.fa

@@ -0,0 +1,43 @@
+>species4|gene3
+MIQIVNDPPVFDPENPQEKGIASRDASLAEGEKKYAATPAYRQDAFGDESNAEVKYKVMK
+WWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVILLVSLGIVATYTGYVLGQFKLKYPWV
+HNMGLAGEVVFGSWGREILGAAQMLFLVFIMASHILTFVIAMNTLTDHGTCSIVFGVGGM
+IISFILSLPRTLAKMSWLSLVSFISIISAVIICMIGVIIKHPGGKVMATVDTDLVHGFSA
+VTNIVFAFSGHAAYFGLMAELKDPRDFPKALMLLQSVDVCLYIIAAIVIYVYGGDAISSP
+ALGSADPIVSKVAYGIALPTIIIAGVINGHVAIKYVYLRIFADKKERIHKRDWVAVSSWV
+AIALSLWTVAWIIAEAIPVFSNLLSLITALFASWFTYGLSGIFWLYLNWGKYLSSPRKMF
+LTIVNLFCLVFGAVLCGLGLYVSGKAIHDNPSSVSFSCANNA
+>species2|gene3
+MIQSVNDPPLSNPENLQEKGIASRDASLAEDEKKYAATLAYRQDAFGDESNAEVKYKVMK
+WWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVILLVSLGIIATYTGYVLGQFKLQYPWV
+HNMGLAGEVVFGSWGREILGAAQMLLLVFIMASHILTFVIAMNTLTDHGTCSIVFGVAGL
+IVSFILSLPRTLAKMSWLSLVSFISIISAVIICMIGVIIKHPGGKVMATVDTDLVHGFSA
+VTNIVFAFSGHAAYFGLMAELKDPRDFPKALMLLQSVDVCLYIIAAIVIYVYGGDEIASP
+ALGSADPLISKVAYGIALPTIIIAGVINGHVAIKYVYLRIFANKKERIHKRDWVAVSSWV
+AIALSLWTVAWIIAEAIPVFSNLLSLITALFASWFTYGLSGIFWLYLNRGQYLSSPRKMF
+LTIVNLFCLVFGAVLCGLGLYVSGKAIHDNPSSMSFSCANNA
+>species1|gene3
+MTQIVNVPPVSDLENPQEKGTSHDASLAEDEKKYDATPAYRQDAFGDESNAEVKYKVMKW
+CIISAVIICMIGVIIKHPGGKVMATVDTDLVHGFSAVTNIVFAFSGHAAYFGLMAELKDP
+RDFPKALMLLQSVDVCLYIIAAIVIYVYGGDAISSPALGSADPIVSKVAYGIALPTIIIA
+GVINGHVAIKYVYIRIFAGKKERIHKRDWVAVSSWVAIALSLWTVAWIIAEAIPVFSNLL
+SLITALFASWFTYGLSGIFWLYLNWGKYLSSPRKMFLTVVNLFCLVFGAVLCGLGLYVSG
+KAIHDNPSSASFSCANNA
+>species3|gene5
+MRSSEIYPAPPTAADQELWEEKEVSTKQSSLEIGENKDFALHQTQDAFGNEEFAEVKYKV
+LKWWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVIILVCLGALATYTGYVIGQFKWRYP
+HICSMADAGEVLAGRFGRELLGFAQIIFLVFIMASHLLTFTIAMNDLTNHGTCSIVFGVV
+GLAISFVCTLPRTLEKMSWLSLISFISILSSVFITMIGVGISHPGKVIEATVKTDLIHGF
+TAVANIVFAFSGHAAFFSLAAELKNPADYPKALMLLQSVDITLYLVAAIVIYCYGGSTVT
+SPALGSASTVVSKVAYGIALPTIIIAGVINGHVSAKSVYVRIFRGTDHMHKRSWIAVGSW
+TAIVLALWVLAWIIAEAIPVFNKLLSLVTALFASWFTFGLSAIFWFYMNHGQWFSSPKKV
+ALSAVNLLALGVGCCLCGLGLYVSGKAIHDDPHHASFTCMSTV
+>species0|gene6
+MRSSEIYPANPTAADQELWEEKEVSTKQSSLEIGENKDFALHQTQDAFGNEEFAEVKYKV
+LKWWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVIILVCLGALATYTGYVIGQFKWRYP
+HICSMADAGEVLAGRFGRELLGFAQIIFLVFIMASHLLTFTIAMNDLTNHGTCSIVFGVV
+GLAISFVCTLPRTLEKMSWLSLISFISILSSVFITMIGVGISHPGKVIEATVKTDLIHGF
+TAVANIVFAFSGHAAFFSLAAELKNPADYPKALMLLQSVDITLYLVAAIVIYCYGGSTVT
+SPALGSASTVVSKVAYGIALPTIIIAGVINGHVSAKSVYVRIFRGTDHMHKRSWIAVGSW
+TAIVLALWVLAWIIAEAIPVFNKLLSLVTALFASWFTFGLSAIFWFYMNHGQWFSSPKKV
+ALSAVNLLALGVGCCLCGLGLYVSGKAIHDDPHHASFTCMSTV