diff --git a/docs/usage/index.rst b/docs/usage/index.rst index 084576d8..5eaa45f8 100644 --- a/docs/usage/index.rst +++ b/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 + +
diff --git a/orthosnap/helper.py b/orthosnap/helper.py index 1efc7d24..dd13cb14 100644 --- a/orthosnap/helper.py +++ b/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 diff --git a/orthosnap/orthosnap.py b/orthosnap/orthosnap.py index f79d7d82..161f6563 100644 --- a/orthosnap/orthosnap.py +++ b/orthosnap/orthosnap.py @@ -150,7 +150,6 @@ def execute( fasta, output_path, subgroup_counter, - assigned_tips, ) write_output_stats( diff --git a/orthosnap/version.py b/orthosnap/version.py index c68196d1..67bc602a 100644 --- a/orthosnap/version.py +++ b/orthosnap/version.py @@ -1 +1 @@ -__version__ = "1.2.0" +__version__ = "1.3.0" diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.inparalog_report.txt b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.inparalog_report.txt new file mode 100644 index 00000000..1076fb74 --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.0.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.0.fa new file mode 100644 index 00000000..04add3e8 --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.1.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.1.fa new file mode 100644 index 00000000..0593e1f5 --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.2.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.2.fa new file mode 100644 index 00000000..ad2ca65d --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.3.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.3.fa new file mode 100644 index 00000000..f0a73b40 --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.4.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.4.fa new file mode 100644 index 00000000..761f8235 --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.5.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.5.fa new file mode 100644 index 00000000..f5abf54c --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.6.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.6.fa new file mode 100644 index 00000000..349dcedf --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.7.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.7.fa new file mode 100644 index 00000000..c162b6be --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.8.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.8.fa new file mode 100644 index 00000000..746d9880 --- /dev/null +++ b/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 diff --git a/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.9.fa b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.9.fa new file mode 100644 index 00000000..7d9fcfd7 --- /dev/null +++ b/tests/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.9.fa @@ -0,0 +1,43 @@ +>species4|gene5 +MGSMHEAGSRPAADADMDTDRVHPEAVSNSERDFEKQDSKPEYRDAFGDEEYAEVKYKTL +SWWQCGFLMVAETVSLGILSLPAVVAALGLVPAIILLVALGLMSTYTGYTIGQFKWAYPH +IHSMGDAGEVIMGRFGRELFGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVG +LVISFVLCLPRTLAKVSFLSVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAF +LAVCNIVFSFCRLFLHFISFMDRTDRTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCL +YIVAAVVIYCYAGDDVTSPALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMW +RHSDRMHKRDLVATGSWVLIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSAL +FWLYLNKGRFFSTPMKTALTILNVVIMGIACCICGLGLYVSGKALHDDPSSASFSCANNA +>species2|gene0 +MGSMHEAGSRPAAGADMDTDRVHPEAVSDNERDFEKQDSKPEYQDAFGDEEYAEVKYKTL +SWCVFSAVLIVMIAVGVQRPWHGGLNATVDTNLYKAFLAVCNIVFSFCRLFLHFSSFMDR +TNKTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIIAAVVIYCYAGDDVTSPALGS +ASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWRHSDRMHKRDLVATGSWVLIGLA +TWIVAWIIAEAIPVFNNLLSLVREVLVVICTMIWERVLIAPSVTAFRQPGTPDQPTEHLF +PLALFVATRDPRSIG +>species1|gene5 +MGSMLEAGSRPAADAEMDTDRVHPEAVSDGERDFEKQDSKPEYQDAFGDEEYAEVKYKTL +SWCHGCRDSVTGYSLPASGGGRLGPCPFKWAYPHIHSMGDAGEVIMGRFGRELFGTGQLL +LVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFLSVASFIS +VFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSFSGHVAFFGFMAELKNP +RDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSPALGSASIVVKKVAYGIALPTIIIG +GVVNGHVACKYIYVRMWRHSDRMHKRDLVATGSWVLIGLATWIVAWIIAEAIPVFNNLLS +LVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTALTILNVVIMGIACCICGLGLYVSGK +ALHDDPSSASFSCANNA +>species3|gene6 +MAHPTGDKVDSHLNVQTGQFFQDGREEPYLHDAEEKQDEKKGSPIYNDTFGDEEYAEVKY +KVLSWWQCGFLMVAETVSLGILSLPAVVATLGLAPAIVLIVGLGLLATYTGYVIGQFRWR +YPHVQNLADAGEILFGSIGREIFGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFG +VVGLVICFLLGLPRTSANVSYLSVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLY +EAFLAVCNIVFSFSGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGP +NVTSPALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFRHGDRMHSRDLLAT +GSWVGIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSP +RKIALTIFNVIIIGIAACICGLGLYVSGRSLHDDANGSSFSCASNA +>species0|gene2 +MAHPTGDKVDSHLNVQTGQFFQDGREEPYLHDAEEKQDEKKGSPIYNDTFGDEEYAEVKY +KVLSWWQCGFLMVAETVSLGILSLPAVVATLGLAPAIVLIVGLGLLATYTGYVIGQFRWR +YPHVQNLADAGEILFGSIGREIFGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFG +VVGLVICFLLGLPRTSANVSYLSVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLY +EAFLAVCNIVFSFSGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGP +NVTSPALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFRHGDRMHSRDLLAT +GSWVGIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSP +RKIALTFFNVIIIGIAACICGLGLYVSGRSLHDDANGSSFSCASNA diff --git a/tests/integration/integration_test.py b/tests/integration/integration_test.py index 00b32d3e..07b09c33 100644 --- a/tests/integration/integration_test.py +++ b/tests/integration/integration_test.py @@ -961,3 +961,88 @@ def test_inparalog_summary_file(self): output_content = out_file.read() assert expected_content == output_content + + def test_default_param_fake_ogs_inparalog_report_occupancy_1(self): + """""" + kwargs = dict( + tree=f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes_tree.tre", + fasta=f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes.faa", + support=80, + occupancy=1.0, + rooted=False, + snap_trees=False, + inparalog_to_keep=InparalogToKeep.longest_seq_len, + output_path=f"{here.parent.parent}/samples/dataset/", + report_inparalog_handling=False, + ) + execute(**kwargs) + + with open( + f"{here.parent.parent}/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.0.fa", + "r", + ) as expected: + expected_content = expected.read() + + with open( + f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.0.fa", + "r", + ) as out_file: + output_content = out_file.read() + + assert expected_content == output_content + + with open( + f"{here.parent.parent}/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.1.fa", + "r", + ) as expected: + expected_content = expected.read() + + with open( + f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.1.fa", + "r", + ) as out_file: + output_content = out_file.read() + + assert expected_content == output_content + + with open( + f"{here.parent.parent}/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.2.fa", + "r", + ) as expected: + expected_content = expected.read() + + with open( + f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.2.fa", + "r", + ) as out_file: + output_content = out_file.read() + + assert expected_content == output_content + + with open( + f"{here.parent.parent}/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.3.fa", + "r", + ) as expected: + expected_content = expected.read() + + with open( + f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.3.fa", + "r", + ) as out_file: + output_content = out_file.read() + + assert expected_content == output_content + + with open( + f"{here.parent.parent}/expected/fake_ogs/fake_orthologous_group_of_genes.faa.orthosnap.4.fa", + "r", + ) as expected: + expected_content = expected.read() + + with open( + f"{here.parent.parent}/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.4.fa", + "r", + ) as out_file: + output_content = out_file.read() + + assert expected_content == output_content diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa new file mode 100644 index 00000000..14faf626 --- /dev/null +++ b/tests/samples/dataset/fake_orthologous_group_of_genes.faa @@ -0,0 +1,402 @@ +>species0|gene0-duplicate_copy_0 +MFGAVAAGSEESPQAPRCISTRSSSFRVYLSAWNFGMSPERVTTEPLHSPDWDNDWLRQL +AGDIVAGSLSATIIAPITTVIDRSVVERLSSNRSILHTLRTHAICSILKPRKFYFSRPFF +IAWSLYAATYATANATDTSLEHLSKVTEKSTTASLVPTFSFLPTYVVNVCLGILKDIRFS +QIYGHPEGRLKQPPPIPRLAYMAFLFRDSITISSSFTLAPQVASLVPDWITADPHTKRTV +TQLALPALVQYVNTPFHMIALDVIARPQVATIAERSVTIRRGDLAEILNSPAYDYGQDVE +KKKNLDDTSPEDEDPFGNEEFAEVKYRTMGWWKTGILMVAENVSIGILSLPSAFATLGFV +PALIILIGISGISWYTAYILCQFKLRYPQVHSMGDAGEIIMGRFGRELLGIGQLLFLIFV +MASHVLTFTVLMNTITEHGTCTIVFGVIALIVSCVGALPRTMDKVYWMSIASFLSIVAAT +MATMIAVGVEYKGHIPLAVTTHLSFNEEFLAVSNLFFAYVGHASFFGFISEMDKPREFTK +SISVLQVIDTSLYIASAVVIYRYVGADVQSPALGSAGPLGKKIAYGLAIPTVLIAGIVNG +HVASKYVYVRVFRGTNHMHERTLLSIGSWVAIGLISWVVAWVIAESIPVFNNLLSLITAL +FGCWFAYGFPAIFWFTLNKGQWFASSRKIFLTLSNTFILAMAITLCGLGLYVSGDAISKD +SGSGVWTCANNAV +>species0|gene0-duplicate_copy_1 +MFGAVAAGSEESPQAPRCISTRSSSFRVYLSAWNFGMSPERVTTEPLHSPDWDNDWLRQL +AGDIVAGSLSATIIAPITTVIDRSVVERLSSNRSILHTLRTHAICSILKPRKFYFSRPFF +IAWSLYAATYATANATDTSLEHLSKVTEKSTTASLVPTFSFLPTYVVNVCLGILKDIRFS +QIYGHPEGRLKQPPPIPRLAYMAFLFRDSITISSSFTLAPQVASLVPDWITADPHTKRTV +TQLALPALVQYVNTPFHMIALDVIARPQVATIAERSVTIRRGDLAEILNSPAYDYGQDVE +KKKNLDDTSPEDEDPFGNEEFAEVKYRTMGWWKTGILMVAENVSIGILSLPSAFATLGFV +PALIILIGISGISWYTAYILCQFKLRYPQVHSMGDAGEIIMGRFGRELLGIGQLLFLIFV +MASHVLTFTVLMNTITEHGTCTIVFGVIALIVSCVGALPRTMDKVYWMSIASFLSIVAAT +MATMIAVGVEYKGHIPLAVTTHLSFNEEFLAVSNLFFAYVGHASFFGFISEMDKPREFTK +SISVLQVIDTSLYIASAVVIYRYVGADVQSPALGSAGPLGKKIAYGLAIPTVLIAGIVNG +HVASKYVYVRVFRGTNHMHERTLLSIGSWVAIGLISWVVAWVIAESIPVFNNLLSLITAL +FGCWFAYGFPAIFWFTLNKGQWFASSRKIFLTLSNTFILAMAITLCGLGLYVSGDAISKD +SGSGVWTCANNAVTTTTTT +>species0|gene0-duplicate_copy_2 +MFGAVAAGSEESPQAPRCISTRSSSFRVYLSAWNFGMSPERVTTEPLHSPDWDNDWLRQL +AGDIVAGSLSATIIAPITTVIDRSVVERLSSNRSILHTLRTHAICSILKPRKFYFSRPFF +IAWSLYAATYATANATDTSLEHLSKVTEKSTTASLVPTFSFLPTYVVNVCLGILKDIRFS +QIYGHPEGRLKQPPPIPRLAYMAFLFRDSITISSSFTLAPQVASLVPDWITADPHTKRTV +TQLALPALVQYVNTPFHMIALDVIARPQVATIAERSVTIRRGDLAEILNSPAYDYGQDVE +KKKNLDDTSPEDEDPFGNEEFAEVKYRTMGWWKTGILMVAENVSIGILSLPSAFATLGFV +PALIILIGISGISWYTAYILCQFKLRYPQVHSMGDAGEIIMGRFGRELLGIGQLLFLIFV +MASHVLTFTVLMNTITEHGTCTIVFGVIALIVSCVGALPRTMDKVYWMSIASFLSIVAAT +MATMIAVGVEYKGHIPLAVTTHLSFNEEFLAVSNLFFAYVGHASFFGFISEMDKPREFTK +SISVLQVIDTSLYIASAVVIYRYVGADVQSPALGSAGPLGKKIAYGLAIPTVLIAGIVNG +HVASKYVYVRVFRGTNHMHERTLLSIGSWVAIGLISWVVAWVIAESIPVFNNLLSLITAL +FGCWFAYGFPAIFWFTLNKGQWFASSRKIFLTLSNTFILAMAITLCGLGLYVSGDAISKD +SGSGVWTCANNAVTT +>species0|gene1 +MAPTTRDLEALAVHHDSDIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCG +ILMIAENISLGILSLPSAVATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGD +AGEILFGRIGREILFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFI +GALPRTMGKVYWMSLASCTSITVATIVTMVAIAVQAPDHVQVDITTHPSFSTAFLSVTNI +VFAFIAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASPALSS +AGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWRGSPQMHTNSLAAVGSWVAIALG +VWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIFLTIVN +LVIFGIACAICGLGLYVSGKAIHDSSSSASWTCANNAST +>species0|gene2 +MAHPTGDKVDSHLNVQTGQFFQDGREEPYLHDAEEKQDEKKGSPIYNDTFGDEEYAEVKY +KVLSWWQCGFLMVAETVSLGILSLPAVVATLGLAPAIVLIVGLGLLATYTGYVIGQFRWR +YPHVQNLADAGEILFGSIGREIFGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFG +VVGLVICFLLGLPRTSANVSYLSVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLY +EAFLAVCNIVFSFSGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGP +NVTSPALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFRHGDRMHSRDLLAT +GSWVGIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSP +RKIALTFFNVIIIGIAACICGLGLYVSGRSLHDDANGSSFSCASNA +>species0|gene3 +MPVTFEVLTIPVMIAETISLRILAFPKVLATLGLLPGIAVIIGVGVLTTYTGLVIGDFKC +RYPQAHSMADAGTILWGRIGCEILGAAQLIFFVFIMGSHILTFSVMMSVLTGYSGCTVLF +SVAGGLPSNVFTIPRRLESLSFLSSVSFASVLGAVFASMSIISIANIVFAYAGHVAFFTF +FSELRGVRDYPRALALLRVSEVTLYMVTAIVIHVLVGNDVASPSLNSVSPIFKKISYGIA +IQTVGGPSKGVLLCRPADRISQIVIAGAVNAHVAMKSIYLRMFHSRNAMHSRPLGAISLW +AVVCVTLWFLAWVVSESTPVFNDILGLAMTPVLQSSFLASWFIFNLPGVFWLYLNVHGKP +LSWKQIILIGFNCIIVTIGVVMCIFGGILIYQIN +>species0|gene4 +MRLLNKVALVTGSSSGIGRAIALRYAREGAKVACADITPTARSPVPNELDITTHDAISQE +GGQAFFLQTDVGDASQMENAVLKTAQQFGRLDIMVNNAGVSLESRTPARIHETTNELYDT +TMRINTRSVFLGSKYAITQMLKQDPHPSGDRGWIINLSSILGIVAATENPSYCASKGAVS +NLTRQVALDYARDRIHANAICPGYTRTAIYEETTEYMHAAADLIRRHPFNGPGLPDDIAR +VAVVLASEDASWMTGAVVPVDGGYTARFSFASIGTLVAVTTAALLRPSICNQTALSFPVT +MRLDGVAPPPDAVEPKSQREKDEDVEDLKAIDNAPEVDAFGDEANAEVKYKTLKWWQCGM +FMIAESVSLGVLSLPATMTALGLVPSLILIIGLGILALYTGYVIGQFRERHPYIHNLADA +GEILMGSFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVAFVICLVL +SLPRTIKNLTYISTASFLSIFSAVMITMIGVGVQYKGGQNISITTETNLYTAFSGVTQIM +FAYCAHVAFFGLIAEMEEPKDFPKALCLLQGFEISLYVTAAIVIYYYVGNGVDSPALGSA +GPVLKKVAYGMAIPTIIGAGVVNGHVGLKYIYVRIFRKSGRMHKNDWVSVGSWIGIGVTC +WVIAWIIGEGIPSFSNLVSLISSLFASWFSFGLPGAYWLHMNYGQWWSSPRKCALTIINM +LIFAIGGAMCGLGLYASGKAIHDDSSRSSFSCANNA +>species0|gene5 +MEAVHDSPPPYATEGIDEKKEDISQVEQNLKPGLEESDAFGNEEFAEIKYKTLKWWQCGL +LMICESVSLGVLSLPAAVATLGFVPAVILIVGLGILATYTGYNIGLFRERYPHIQNLADA +GEILMGPFGRELFGLGQFLFCIFVMGSHLLTFRVMMNTITDHGTCSIVFSVVGMIISMVL +SIPRTMKGMTWISFASFLSIFSAVMITMIGVGVEKHPGRIIEATVDTTLYTAFTAVSNIV +FAYCAHVAFFGLIAEMEKPKDFKKSLFMLQAFEISLYVTAACVIYYYVGKDVQSPALSSA +GPLLKKVAYGIAIPTIVGAGVVNGHIGLKYIYFRTCSKSGLIHSRSRRSVAVWIALGLAC +WLVAWIIAEAIPVFSDLNSLISALFASWFSYGLSGIYWLHLNYGQWFASPRKIALTVLNA +AIAVFGLVLCVLGLYASGTAIHNDANSNKIGWPIECWHNREPFRVRHSVRFLLPQALKHT +GKYRAIRTNCWQPAICNHPESFPFGHRLRPNVAMHTRAELATQACDICRKRKVKCNVTSS +STDVPSRCGRCARLDLPCTFLSPSRTRGPKKRSRTGSPAQEQPDWGTGGSRASGAVNYPT +DDVCDRRMFSCIMQDYLDYLYPLIPIVHRPSFQQSLQEDRDREDSGFLGLVTAIAAVVIA +TMPSRFHFYRSATPPLRFTSRRDMVRHCYDKILRLRDSTYFDHINFQKFAISYLLYAAFR +QLGDHNWSRMLDVEATQIARLLNLHRISEYDGLNCIETQLRKKGFWLIFYGFVHNQLQNV +LGERLSYLDPILLHSINPEDLMPLEVDDEMIFENEVLMPPSHTPCLVTGFILHSRVFWAA +IRSTCPESPAEPCPCVRARDAAVQVAYIQDRLHSLRFLLEDIPPLLRPWQPPDSQAIAHE +GGSTGVTEMTQSHFASMRANLHVTHLWLQSLLVDQLEAAQAHKSEPSLVSTNHVQPMVDA +KALWLQREGLCRQLFCILYSLPQINLEANGLHLAYKVRDIAAGLLVCPFHPAGPEAERAT +EYLRQSTDILSRLDSSEGMVTMHLQTWIDTDRIKSS +>species0|gene6 +MRSSEIYPANPTAADQELWEEKEVSTKQSSLEIGENKDFALHQTQDAFGNEEFAEVKYKV +LKWWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVIILVCLGALATYTGYVIGQFKWRYP +HICSMADAGEVLAGRFGRELLGFAQIIFLVFIMASHLLTFTIAMNDLTNHGTCSIVFGVV +GLAISFVCTLPRTLEKMSWLSLISFISILSSVFITMIGVGISHPGKVIEATVKTDLIHGF +TAVANIVFAFSGHAAFFSLAAELKNPADYPKALMLLQSVDITLYLVAAIVIYCYGGSTVT +SPALGSASTVVSKVAYGIALPTIIIAGVINGHVSAKSVYVRIFRGTDHMHKRSWIAVGSW +TAIVLALWVLAWIIAEAIPVFNKLLSLVTALFASWFTFGLSAIFWFYMNHGQWFSSPKKV +ALSAVNLLALGVGCCLCGLGLYVSGKAIHDDPHHASFTCMSTV +>species0|gene7 +MSTLDVKDIENGPARRVEEEGGMWENDMEKTPSVERDPFGNEAVGEVHYKTLDWWQSGML +MIAETVSLGVLSLPATVAEVGLIPAIILIVGMGIIATYSGYVIGQFRARYPFIHSMADAG +EVLCGRYGRMFTEFAQLVFFMFASGSHLVTFTVMMNTLTNHGTCSVVFGVVGLVLSFACS +LPRTMKNVSWLAVTSFLSIFTAVLITMIGVAVEHPNPPPMQLTRSTSFVKGFSAVTNIAF +AYCGHPAFFGFIAEMKEPKDFPKSLCMLQGFEIVFYTVASAVIYRYAGQNVTSPALGSAG +IIVRKVAYGIAIPTIVIAGVVLGHVAIKNVYVRLFRGTDVMHKRSALGIGAWIGLAAGYW +IIAWVIAEAIPVFSDLVSLVSALFASWFSFGLPGVFWLYMYWGNYFTSVRKTLLTLANLA +LFGIGATICVCGLWVSGLSISSDSSGSSFSCANNA +>species0|gene8 +MSPPSAINNPGDPLAEQEKPAGARNTTGTEDPFSHDGVGGVKYRTLAWWQCAMIMVAETI +SLGILSLPSAVASLGLVAAVILIIGLGALATYTGYTLGQFKLRYPHVHSMGDAGEVLMGR +IGREVLGTAQLLFLIFIMGSHLLTFTVMMNTLTDHGTCSIVFGVIGLAVSFAFTLPRTLK +KVSWFSISSFISIIAAVLITMIAIAIQKPGGGRVDAIVDNSFYKAFLAVTNIVFAYAGHV +AFFGFISEMRTPTDYPKTLYMLQGIDTSMYTISAVVIYRYGGRDVASPALGSTSPLMSKI +AYGIAIPTIVIAGVINGHVACKYIYVRLFRGTDRMHQRGLVSIGTWVIIGLVLWTLAWII +AEAIPVFNDLLSLITALFASWFTYGLSGIFWLFLNWGRYSSSRRKILLTGLNLLVVVVGG +CLCALGLYVSGKSIHDHPRSSSFSCANNA +>species1|gene0 +MSPDTSDLDLGTRPAVSLNRGEGYKEQPETPDEEPFGDEEGAEVRYRTLEWWFVSPGSAE +GRQSRSDVACEQEMRDRGVILIVGIAILTVYTGCVMGQFKQRYPHVHSIADGGEVLFGWI +GREVLGTGLLLCLVFVMGGHILTFTVMMNTLTDHGTCSIVFGVVGLLISLILSLPRTFKR +MSWLSVISFASIVAAVLVTMIALGVQRPPNVKVEVTRPTSLYRAFLAVTDIVFAYAAHPA +FFGYISEMKTPTDWPKTLCFVEVINTTLYTVTGVVIYRFAGQHVASPALGSSSPLMAKVA +YGIAIPTIVIAGVINGHIACKYIYVRLFRGTEHMHQRSLFAIGTWVAISVVLWTIAWVIA +EAVPEFNNLLSLVLVFVCVSF +>species1|gene1 +MMLEGVPPPSEPIEAKQKDQEKALDDGADLKPIDNTPYVDPFGDEQNAEVKYKTLKWWQC +GMFMIAESVSLGVLSLPATLAALGLVPAIILIVGLGILALYTGYTIGQFRQCYPHIHNLA +DAGEILMGRFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVGMLICM +VLSLPRTIKNLTYISFASFLSIFSAVMITMIGVAVQFKGGANISITTETNLYHAFTGVTN +IVFAYCAHVAFFGLIAEMEDPKEFPKSLCMLQFFEIALYVTAAIVIYYYVGNDVVSPALG +SAGPLLKKVAYGIAIPTIVGAGVVNGHVGLKYIYVRIFRKTGRMHKRDLVSVGSWIAIGL +SCWIIAWIIAEGIPSFTNIVSLISSLFASWFSYGLPGVYWLHINWGRWFSSPRKICLTII +NLLIVCIGATMCGLGLYVSGKAIHDDSSNTSFTCANTAN +>species1|gene2 +MAVSRDLEAPAVVNDPTAYDATVEKKEYADGTPANDPFGNEECGEVKYRVMSWWQCGTLM +VAENISLGILSLPSAVATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQVHSMGDAGE +LLMGRFGRELFGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGAL +PRTMGKVYWMSMASCISIVTATVVTMIAIGVQAPEHVHVDATTEVSFQDAFLAVTNIIFA +YIAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGP +VMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALSVWV +VAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFLI +LAFACALCGMGLYVSGKSIHDSSSKASWTCKNNAT +>species1|gene3 +MTQIVNVPPVSDLENPQEKGTSHDASLAEDEKKYDATPAYRQDAFGDESNAEVKYKVMKW +CIISAVIICMIGVIIKHPGGKVMATVDTDLVHGFSAVTNIVFAFSGHAAYFGLMAELKDP +RDFPKALMLLQSVDVCLYIIAAIVIYVYGGDAISSPALGSADPIVSKVAYGIALPTIIIA +GVINGHVAIKYVYIRIFAGKKERIHKRDWVAVSSWVAIALSLWTVAWIIAEAIPVFSNLL +SLITALFASWFTYGLSGIFWLYLNWGKYLSSPRKMFLTVVNLFCLVFGAVLCGLGLYVSG +KAIHDNPSSASFSCANNA +>species1|gene4 +MEAINANPPAYRTEKVEETKYTSDYEEEGQLKTGQVADAFGNEESAEIKYKTLKWWQCGL +LMICESVSLGVLSLPAAVATLGLVPAVILIVGLGLLATYTGYNIGLFRERYPKIQNLGDA +GEILMGPIGREIFGLGQFLFFIFVMGSHILTFRVMMNTITEHGTCSIVFSVVGMVISMVL +SIPRTMKGLTWISFASFLSIFGAVMITMISVGVQDHPHRIIEATVDTTLYSGFQAVSNIV +FAYCAHVAFFGLIAEMENPRDFKKSLFMLQSFEICLYLTAAVVIYYFVGKDVASPALISA +GPVMKKVAFGIAIPTIVGAGVVNGHVGLKYIYFRLCHKSDLIHSRSKRSVGIWIGLGLTC +WVVAWVIAEAIPVFSDLNGLISALFASWFSYGLSGIYWLHLNYGHWFASPRKILLTILNI +SIALFGLALCVLGLYASGTAIHNDTSSSSFSCANTDA +>species1|gene5 +MGSMLEAGSRPAADAEMDTDRVHPEAVSDGERDFEKQDSKPEYQDAFGDEEYAEVKYKTL +SWCHGCRDSVTGYSLPASGGGRLGPCPFKWAYPHIHSMGDAGEVIMGRFGRELFGTGQLL +LVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFLSVASFIS +VFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSFSGHVAFFGFMAELKNP +RDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSPALGSASIVVKKVAYGIALPTIIIG +GVVNGHVACKYIYVRMWRHSDRMHKRDLVATGSWVLIGLATWIVAWIIAEAIPVFNNLLS +LVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTALTILNVVIMGIACCICGLGLYVSGK +ALHDDPSSASFSCANNA +>species2|gene0 +MGSMHEAGSRPAAGADMDTDRVHPEAVSDNERDFEKQDSKPEYQDAFGDEEYAEVKYKTL +SWCVFSAVLIVMIAVGVQRPWHGGLNATVDTNLYKAFLAVCNIVFSFCRLFLHFSSFMDR +TNKTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIIAAVVIYCYAGDDVTSPALGS +ASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWRHSDRMHKRDLVATGSWVLIGLA +TWIVAWIIAEAIPVFNNLLSLVREVLVVICTMIWERVLIAPSVTAFRQPGTPDQPTEHLF +PLALFVATRDPRSIG +>species2|gene1 +MKAESQTQAQKPEDMDQKKEEPMPPVRQDAFGDEEFAEVKYKVLKWWQGGLLMVAETISL +GILSLPAAVGTVGLAPGLAILISMGILASYNGYVIGQIKLRFPHITSMSDAGEVLLGPFG +RELLNAAQILLLIFIMASHILTFTVAFNVMTGHATCSIVFGVVGAVISCLLSLPRTLEKV +SWLSLVSFVSIFAAVMVTMVSIGIIKPTSTWAVAKHTDLVTAFGGVTNMVFAYASHNSFF +TFIAELRDPREFPKALALLQSIDISLYVVAAVVIYYFAGDGVTSPALGSAGPLISKAAYG +IALPTIVIAGVINGHIAAKAIYLRMFSGTDRIHKRDWIAVGSWIGIMAVLWTISWIIAEA +IPVFNDLIGLIAALFLSWFTFGLPGVFWLYMNKGIWFLSRRKLFLTVVNVASVCIGLVVV +SIYILGSPTVLGLIDQCALGLYASGVSINHNPAGSVFSCGARS +>species2|gene2-duplicate_copy_0 +MMLWLKRRNMLMGRRQMTRLEMKNAERSNIVSCRGVMVAENISLGILSLSSAVATLGIVP +AVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGELLMGRFGRELFGIGQLLFLIFLM +ASHILTFSVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWMSMASCISIVTATV +VTMIAIGVQAPDHVHVNVTTKVSFQDAFLAVTNIIFAYIAHVAFFGFISEMHDPRDFPKS +LTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGPLMKKVAYGLAIPTVVIAGVVFGH +VACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALGVWVVAWVIAESIPVFNELLSLISSLF +GSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFFILAFACALCGMGLYVSGKSIHDSS +SKASWTCKNNAT +>species2|gene2-duplicate_copy_1 +MMLWLKRRNMLMGRRQMTRLEMKNAERSNIVSCRGVMVAENISLGILSLSSAVATLGIVP +AVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGELLMGRFGRELFGIGQLLFLIFLM +ASHILTFSVVFNTITNHGTCTIVFGVVGLVVSFIGALPRTMGKVYWMSMASCISIVTATV +VTMIAIGVQAPDHVHVNVTTKVSFQDAFLAVTNIIFAYIAHVAFFGFISEMHDPRDFPKS +LTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGPLMKKVAYGLAIPTVVIAGVVFGH +VACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALGVWVVAWVIAESIPVFNELLSLISSLF +GSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFFILAFACALCGMGLYVSGKSIHDSS +SKASWTCKNNAT +>species2|gene3 +MIQSVNDPPLSNPENLQEKGIASRDASLAEDEKKYAATLAYRQDAFGDESNAEVKYKVMK +WWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVILLVSLGIIATYTGYVLGQFKLQYPWV +HNMGLAGEVVFGSWGREILGAAQMLLLVFIMASHILTFVIAMNTLTDHGTCSIVFGVAGL +IVSFILSLPRTLAKMSWLSLVSFISIISAVIICMIGVIIKHPGGKVMATVDTDLVHGFSA +VTNIVFAFSGHAAYFGLMAELKDPRDFPKALMLLQSVDVCLYIIAAIVIYVYGGDEIASP +ALGSADPLISKVAYGIALPTIIIAGVINGHVAIKYVYLRIFANKKERIHKRDWVAVSSWV +AIALSLWTVAWIIAEAIPVFSNLLSLITALFASWFTYGLSGIFWLYLNRGQYLSSPRKMF +LTIVNLFCLVFGAVLCGLGLYVSGKAIHDNPSSMSFSCANNA +>species2|gene4 +MEAINANPPPYRTEKVEETKYTSDYEEEGQLKTGQVADAFGNEESAEIKYKTLKWWQCGL +LMICESVSLGVLSLPAAVATLGLVPAVILIVGLGLLATYTGYNIGLFRERYPRIQNLGDA +GEILMGPIGREIFGLGQFLFFIFVMGSHILTFRVMMNTVTEHGTCSIVFSVVGMVISMVL +SIPRTMKGLTWISFASFLSIFGAVMITMISVGVQDHPGRIIEATVDTTLYSGFQAVSNIV +FAYCAHVAFFGLIAEMENPRDFKKSLFMLQSFEISLYLTAAVVIYYFVGKDVASPALISA +GPVMKKVAFGIAIPTIVGAGVVNGHVGLKYIYFRLCHKSDLIHRRSKRSVGIWIGLGLTC +WVVAWIIAEAIPVFSDLNGLISALFASWFSYGLSGIYWLHLNYGQWFASPRKILLTILNI +SIALFGLALCVLGLYASGTAIHNDTSSSSFSCANTDA +>species2|gene5 +MSPDTSDLDLETRPAVSLNRGEEYKEQPETPDEEPFGDEDDAEVRYRTLEWWFVSPVMLA +GGTSLGILTLPSAVATLGIVPGVILIVGIAILTVYTGYVMGQFKQRYPHVHSIADGGEVL +FGWVGREILGAGLLLCLVFVMGGHILTFTVMMNTLTDHGTCSVVFGVVGLLISLILSLPR +TFKRMSWLSVISFASIVGAVLVTMIALGVQRPPNVRVEVTRPTSLYRAFLAVTDIVFAYA +AHPAFFGFISEMKTPTDWPKTLCFVEIINTTLYTVTGVVIYRFAGQHVASPALGSTSPLM +AKVAYGTAIPTIVIAGVINGHIACKYIYVRVFRGTEHMHRRSLFAIGTWVVISVVLWTVA +WVIAEAVPEFNNLLSLITSLFCSWFSYGLCGAFWLFINKGLWFSSPRKTFLTIVNFTLLG +MGACLCGLGLYASGRAISEESAGRIFSCASTA +>species2|gene6 +MMLDGVPQPPEPIEAKQNDQEKALDDGADLKPIDNTPYIDPFGDEQNAEVKYKTLKWWTC +AGNVECVSYGMGKRSSRLMIAESVSLGVLSLPATLASLGLVPAIILIVGLGILALYTGYT +IGQFRQCYPHIHNLADAGEILMGRFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHG +TCSIVFSIVGMLICMVLSLPRTIKNLTYISFASFLSIFSAVMITMIGVAVQFKGGSNISV +TAETNLYHAFTGVTNIVFAYCAHVAFFGLIAEMEDPKEFPKALCMLQFFEIALYVTAAIV +IYYYVGNDVVSPALGSAGPLLKKVAYGIAIPTIVGAGVVNGHVGLKYIYVRIFRKTNRMH +KRDLVSVGSWIAIGLSCWIIAWIIAEGIPSFTNIVSLISSLFASWFSYGLPGVYWLHINW +GRWFSSPRKICLTIVNLLIVCIGATMCGLGLYVSGKAIHDDSSNTSFTCANTAS +>species3|gene0 +MQDYLDYLYPLIPIVHRPSFQQSLQQDRDREDSGFLGLVTAIAAVVIATMPSRFHFYRSA +TPPLRFTSRRDMVRHCYDKILRLRDSTYFDHINFQKFAISYLLYAAFRQLGDHNWSRMLD +VEATQIARLLNLHRISEYDGLNCIETQLRKKGFWLIFYGFVHNQLQNVLGERLSYLDPIL +LHSINPEDLMPLEVDDEMIFENEVLMPPSHTPCLVTGFILHSRVFWAAIRSTCPESPAEP +CPCVRARDAAVQVAYIQDRLHSLRFLLEDIPPLLRPWQPPDSQAIAHEGGSTGVTEMTQS +HFASMRANLHVTHLWLQSLLVDQLEAAQAHKSEPSLVSTNHVQPMVDAKALWLQREGLCR +QLFCILYSLPQINLEANGLHLAYKVRDIAAGLLVCPFHAAGPEAERATEYLRQSTDILSR +LDSSEGMVTMHLQTWIDTDRIKSS +>species3|gene1 +MEAVHDSPPPYATEGIDEKKEDISQVEQNLKPGLEESDAFGNEEFAEIKYKTLKWWQCGL +LMICESVSLGVLSLPAAVATLGFVPAVILIVGLGILATYTGYNIGLFRERYPHIQNLADA +GEILMGPFGRELFGLGQFLFCIFVMGSHLLTFRVMMNTITDHGTCSIVFSVVGMIISMVL +SIPRTMKGMTWISFASFLSIFSAVMITMIGVGVEKHPGRIIEATVDTTLYTAFTAVSNIV +FAYCAHVAFFGLIAEMEKPKDFKKSLFMLQAFEISLYVTAACVIYYYVGKDVQSPALSSA +GPLLKKVAYGIAIPTIVGAGVVNGHIGLKYIYFRTCSKSGLIHSRSRRSVAVWIALGLAC +WLVAWIIAEAIPVFSDLNSLISALFASWFSYGLSGIYWLHLNYGQWFASPRKIALTVLNA +AIAVFGLVLCVLGLYASGTAIHNDANSNSFTCANTDS +>species3|gene2 +MSVPMESRDLAEILNSPAYDYGQDVEKKKNLDDTPPEDEDPFGNEEFAEVKYRTMGWWKT +GILMVAENVSIGILSLPSAFATLGFVPALIILIGISGISWYTAYILCQFKLRYPQVHSMG +DAGEIIMGRFGRELLGIGQLLFLIFVMASHVLTFTVLMNTITEHGTCTIVFGVIALIVSC +VGALPRTMDKVYWMSIASFLSIVAATMATMIAVGVEYKGHIPLAVTTHLSFNEEFLAVSN +LFFAYVGHASFFGFISEMDKPREFTKSISVLQVIDTSLYIASAVVIYRYVGADVQSPALG +SAGPLGKKIAYGLAIPTVLIAGIVNGHVASKYVYVRVFRGTNHMHERTLLSIGSWVAIGL +ISWVVAWVIAESIPVFNNLLSLITALFGCWFAYGFPAIFWFTLNKGQWFASSRKIFLTLS +NTFILAMAITLCGLGLYVSGDAISKDSGSGVWTCANNAV +>species3|gene3 +MSPPSAINNPGDPLAEQEKPVGARNTTGTEDPFSHDGVGGVKYRTLAWWQCAMIMVAETI +SLGILSLPSAVASLGLVAAVILILGLGALATYTGYTLGQFKLRYPHVHSMGDAGEVLMGR +IGREVLGTAQLLFLIFIMGSHLLTFTVMMNTLTDHGTCSIVFGVIGLAVSFAFTLPRTLK +KVSWFSISSFISIIAAVLITMIAIAIQKPGGGRVDAIVDNSFYKAFLAVTNIVFAYAGHV +AFFGFISEMRTPTDYPKTLYMLQGIDTSMYTISAVVIYRYGGRDVASPALGSTSPLMSKI +AYGIAIPTIVIAGVINGHVACKYIYVRLFRGTDRMHQRGLVSIGTWVMIGLVLWTLAWII +AEAIPVFNDLLSLITALFASWFTYGLSGIFWLFLNWGRYSSSRRKILLTGLNLLVVVVGG +CLCALGLYVSGKSIHDHPRSSSFSCANNA +>species3|gene4 +MSTLDVKDIENGPARRVEEEGGMWENDMEKTPSVERDPFGNEAVGEVHYKTLDWWQSGML +MIAETVSLGVLSLPATVAEVGLIPAIILIVGMGIIATYSGYVIGQFRARYPFIHSMADAG +EVLCGRYGRMFTEFAQLVFFMFASGXHLVTFTVMMNTLTNHGTCSVVFGVVGLVLSFACS +LPRTMKNVSWLAVTSFLSIFTAVLITMIGVAVEHPNPPPMQLTRSTSFVKGFSAVTNIAF +AYCGHPAFFGFIAEMKEPKDFPKSLCMLQGFEIVFYTVASAVIYRYAGQNVTSPALGSAG +IVVRKVAYGIAIPTIVIAGVVLGHVAIKNVYVRLFRGTDVMHKRSALGIGAWIGLAAGYW +IIAWVIAEAIPVFSDLVSLVSALFASWFSFGLPGVFWLYMYWGNYFTSVRKTLLTLANLA +LFGIGATICVCGLWVSGLSISSDSSGSSFSCANNA +>species3|gene5 +MRSSEIYPAPPTAADQELWEEKEVSTKQSSLEIGENKDFALHQTQDAFGNEEFAEVKYKV +LKWWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVIILVCLGALATYTGYVIGQFKWRYP +HICSMADAGEVLAGRFGRELLGFAQIIFLVFIMASHLLTFTIAMNDLTNHGTCSIVFGVV +GLAISFVCTLPRTLEKMSWLSLISFISILSSVFITMIGVGISHPGKVIEATVKTDLIHGF +TAVANIVFAFSGHAAFFSLAAELKNPADYPKALMLLQSVDITLYLVAAIVIYCYGGSTVT +SPALGSASTVVSKVAYGIALPTIIIAGVINGHVSAKSVYVRIFRGTDHMHKRSWIAVGSW +TAIVLALWVLAWIIAEAIPVFNKLLSLVTALFASWFTFGLSAIFWFYMNHGQWFSSPKKV +ALSAVNLLALGVGCCLCGLGLYVSGKAIHDDPHHASFTCMSTV +>species3|gene6 +MAHPTGDKVDSHLNVQTGQFFQDGREEPYLHDAEEKQDEKKGSPIYNDTFGDEEYAEVKY +KVLSWWQCGFLMVAETVSLGILSLPAVVATLGLAPAIVLIVGLGLLATYTGYVIGQFRWR +YPHVQNLADAGEILFGSIGREIFGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFG +VVGLVICFLLGLPRTSANVSYLSVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLY +EAFLAVCNIVFSFSGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGP +NVTSPALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFRHGDRMHSRDLLAT +GSWVGIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSP +RKIALTIFNVIIIGIAACICGLGLYVSGRSLHDDANGSSFSCASNA +>species3|gene7 +MAPTTRDLEALTVHHDSDIMADDLAEKKVSANESPPENDPFGNEECGEVKYRVMKWWHCG +ILMIAENISLGILSLPSAVATLGIVPSIFLILGLSGISWYTGYVIGQFKLRYPQVHSMGD +AGEILFGRIGREILFFGQLLFCIFLMSSHILTFTVLFNTITGHGTCTIVFGVVGLVVSFI +GALPRTMGKVYWMSLASCTSITVATIVTMVAIAMQAPDHVQVDITTHPSFSTAFLSVTNI +VFAFIAHVAFFGFASEMEDPRDFPKSLAMLQVTDTTMYIVTAMVIYRYAGPDVASPALSS +AGPLMSKVAYGLAIPTVIIAGVVFGHVASKYIYVRVWRGSPQMHTNSLAAVGSWVAIALG +VWVIAWIIAESIPVFNDLLSLISSLFGSWFSYGLPAMFWLVMNRGQYTASPRKIFLTIVN +LVIFGIACAICGLGLYVSGKAIHDSSSSASWTCANNAST +>species3|gene8 +MRLDGVAPPPDAVEPKSQREKDEDVEDLKAINNAPEVDAFGDEANAEVKYKTLKWWQCGM +FMIAESVSLGVLSLPATMTALGLVPSLILIIGLGILALYTGYVIGQFRERHPYIHNLADA +GEILMGSFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVAFVICLVL +SLPRTIKNLTYISTASFLSIFSAVMITMIGVGVQYKGGQNISITTETNLYTAFSGVTQIM +FAYCAHVAFFGLIAEMEEPKDFPKALCLLQGFEISLYVTAAIVIYYYVGNGVDSPALGSA +GPVLKKVAYGMAIPTIIGAGVVNGHVGLKYIYVRIFRKSGRMHKNDWVSVGSWIGIGVTC +WVIAWIIGEGIPSFSNLVSLISSLFASWFSFGLPGAYWLHMNYGQWWSSPRKCALTIINM +LIFAIGGAMCGLGLYASGKAIHDDSSRSSFSCANNA +>species4|gene2-duplicate_copy_0 +MAVSRDLEAPAVVNDPTADDAMVEKKEYADGTPANDPFGNEECGEVRYRVMSWWQCGTLM +VAENISLGILSLPSAVATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGE +LLMGRFGRELFGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGAL +PRTMGKVYWMSMASCISIVTATVVTMIAIGVQAPDHVHVDATTEVSFQDAFLAVTNIIFA +YIAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGP +LMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALGVWV +VAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFLI +LAFACALCGMGLYVSGKSIHDSSSKASWTCKNNAT +>species4|gene2-duplicate_copy_1 +MAVSRDLEAPAVVNDPTADDAMVEKKEYADGTPANDPFGNEECGEVRYRVMSWWQCGTLM +VAENISLGILSLPSAVATLGIVPAVILLLGLSAISWYTGYIMGQFKLRFPQIHSMGDAGE +LLMGRFGRELFGIGQLLFLIFLMASHILTFTVVFNTITNHGTCTIVFGVVGLVVSFIGAL +PRTMGKVYWMSMASCISIVTATVVTMIAIGVQAPDHVHVDATTEVSFQDAFLAVTNIIFA +YIAHVAFFGFISEMHDPRDFPKSLTMLQVVDTSLYIVTAMVIYRYAGPDVASPALSSAGP +LMKKVAYGLAIPTVVIAGVVFGHVACKYIYVRIFRGSAHMHQNSFLAIGSWVAIALGVWV +VAWVIAESIPVFNELLSLISSLFGSWFSYGLPAIFWLVMNKGRWFSTRSKICLTIVNFLI +LAFACALCGMGLYVSGKSIHDSSSKASWTCKNNATTTT +>species4|gene5 +MGSMHEAGSRPAADADMDTDRVHPEAVSNSERDFEKQDSKPEYRDAFGDEEYAEVKYKTL +SWWQCGFLMVAETVSLGILSLPAVVAALGLVPAIILLVALGLMSTYTGYTIGQFKWAYPH +IHSMGDAGEVIMGRFGRELFGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVG +LVISFVLCLPRTLAKVSFLSVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAF +LAVCNIVFSFCRLFLHFISFMDRTDRTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCL +YIVAAVVIYCYAGDDVTSPALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMW +RHSDRMHKRDLVATGSWVLIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSAL +FWLYLNKGRFFSTPMKTALTILNVVIMGIACCICGLGLYVSGKALHDDPSSASFSCANNA +>species4|gene0 +MEAIKANPPAYRTEKVEETKYTSDYEEEGQLKTGQVADAFGNEESAEIKYKTLKWWQCGL +LMICESVSLGVLSLPAAVATLGLVPAVILIVGLGLLATYTGYNIGLFRERYPKIQNLGDA +GEILMGPIGREIFGLGQFLFFIFVMGSHILTFRVMMNTITEHGTCSIVFSVVGMVISMVL +SIPRTMKGLTWISFASFLSIFGAVMITMISVGVQDHPDRIIEATVDTTLYSGFQAVSNIV +FAYCAHVAFFGLIAEMENPRDFKKSLFMLQSFEISLYLTAAVVIYYFVGKDVASPALISA +GPVMKKVAFGIAIPTIVGAGVVNGHVGLKYIYFRLCHKSDLIHSRSKRSVGIWIGLGLTC +WVVAWVIAEAIPVFSDLNGLISALFASWFSYGLSGIYWLHLNYGQWFASPRKILLTILNI +SIALFGLALCVLGLYASGTAIHNDTSSSSFSCANTDA +>species4|gene4 +MMLEGIPPPPEPIEAKQNDQEKALDDGADLKPIDNTPYIDPFGDEQNAEVKYKTLKWWQC +GMFMIAESVSLGVLSLPATLAALGLVPAIILIVGLGILALYTGYTIGQFRQCYPHIHNLA +DAGEILMGRFGRELFGLGQILFSIFIMGSHIVTFTVMMNTITDHGTCSIVFSIVGMLICM +VLSLPRTIKNLTYISFASFLSIFSAVMITMIGVAVQFKGGSNISITAETNLYHAFTGVTN +IVFAYCAHVAFFGLIAEMEDPKEFPKSLCMLQFFEIALYVTAAIVIYYYVGNDVVSPALG +SAGPLLKKVAYGIAIPTIVGAGVVNGHVGLKYIYVRIFRKTGRMHKRDLVSVGSWIAIGL +SCWIIAWIIAEGIPSFTNIVSLISSLFASWFSYGLPGVYWLHINWGRWFSSPRKICLTII +NLLVVGIGATMCGLGLYVSGKAIHDDSSNTSFTCANTAN +>species4|gene1 +MSPDTSDLDLETRPAVSLNRGEGYKEQPETPDEEPFGNEEGAEVRYRTLEWWFVSPGSAE +GRQSRSDVACEQEMRDSHAGWGHIARHPNASLGCGDTGNRPVGLPGVILIVGIAILTVYT +GCVMGQFKQRYPHVHSIADGGEVLFGWIGREVLGAGLLLCLVFVMGGHILTFTVMMNTLT +DHGTCSVVFGVVGLLISLILSLPRTFKRMSWLSVISFASIVAAVLVTMIALGVQRPPNVK +VEVTRPTSLYRAFLAVTDIVFAYAAHPAFFGYISEMKTPTDWPKTLCFVEVINTTLYTVT +GVVIYRFAGQHVASPALGSSSPLMAKVAYGIAIPTIVIAGVINGHIACKYIYVRLFRGTE +RMHQRSLFSIGTWVAISVVLWTIAWVIAEAVPEFNNLLSLITSLFCSWFSYGLCGAFWLF +INQGLWFSSPRKTFLTIVNFTLLGMGACLCGLGLYASGRAISEESAGRSFSCASTA +>species4|gene3 +MIQIVNDPPVFDPENPQEKGIASRDASLAEGEKKYAATPAYRQDAFGDESNAEVKYKVMK +WWQCGLLMVAETVSLGVLSLPAAVAGLGLVPSVILLVSLGIVATYTGYVLGQFKLKYPWV +HNMGLAGEVVFGSWGREILGAAQMLFLVFIMASHILTFVIAMNTLTDHGTCSIVFGVGGM +IISFILSLPRTLAKMSWLSLVSFISIISAVIICMIGVIIKHPGGKVMATVDTDLVHGFSA +VTNIVFAFSGHAAYFGLMAELKDPRDFPKALMLLQSVDVCLYIIAAIVIYVYGGDAISSP +ALGSADPIVSKVAYGIALPTIIIAGVINGHVAIKYVYLRIFADKKERIHKRDWVAVSSWV +AIALSLWTVAWIIAEAIPVFSNLLSLITALFASWFTYGLSGIFWLYLNWGKYLSSPRKMF +LTIVNLFCLVFGAVLCGLGLYVSGKAIHDNPSSVSFSCANNA +>species4|gene6 +MNAESQTQPQKPEDMDQKKEESMPPVRQDAFGDEEFAEVKYKVLKWWQGGLLMVAETISL +GILSLPAAVGTVGLAPGLAILISMGILASYNGYVIGQIKLRIPHISSMSDAGEVLLGPFG +RELLNAAQILLLIFIMASHILTFTVAFNVITGHATCSIVFGIVGAVISCLLSLPRTLEKV +SWLSLVSFVSIFVAVMVTMVSIGIIKPTSTWAVAKNTDLVTGFGGVTNMVFAYASHNSFF +TFIAELRDPREFPKALALLQSIDISLYIIAAVVIYYFAGDGVASPALGSAGPLISKIAYG +IALPTIIIAGVINGHIAAKAIYLRMFSGTDRIHKRDWVAVGSWIGIMAVLWTISWIIAEA +IPVFNDLIGLIAALFLSWFTFGLPGVFWLYMNKGMWFLSRRKIFLTVVNVSSVCIGLVVC +ALGLYASGVSIHQNPAGSVFSCGARS diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.inparalog_report.txt b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.inparalog_report.txt new file mode 100644 index 00000000..1076fb74 --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.0.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.0.fa new file mode 100644 index 00000000..04add3e8 --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.1.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.1.fa new file mode 100644 index 00000000..0593e1f5 --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.2.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.2.fa new file mode 100644 index 00000000..ad2ca65d --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.3.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.3.fa new file mode 100644 index 00000000..f0a73b40 --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.4.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.4.fa new file mode 100644 index 00000000..761f8235 --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.5.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.5.fa new file mode 100644 index 00000000..f5abf54c --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.6.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.6.fa new file mode 100644 index 00000000..349dcedf --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.7.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.7.fa new file mode 100644 index 00000000..c162b6be --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.8.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.8.fa new file mode 100644 index 00000000..746d9880 --- /dev/null +++ b/tests/samples/dataset/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 diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.9.fa b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.9.fa new file mode 100644 index 00000000..7d9fcfd7 --- /dev/null +++ b/tests/samples/dataset/fake_orthologous_group_of_genes.faa.orthosnap.9.fa @@ -0,0 +1,43 @@ +>species4|gene5 +MGSMHEAGSRPAADADMDTDRVHPEAVSNSERDFEKQDSKPEYRDAFGDEEYAEVKYKTL +SWWQCGFLMVAETVSLGILSLPAVVAALGLVPAIILLVALGLMSTYTGYTIGQFKWAYPH +IHSMGDAGEVIMGRFGRELFGTGQLLLVVFIMASHILTFTVAMNSITDHGTCSIVFGVVG +LVISFVLCLPRTLAKVSFLSVASFISVFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAF +LAVCNIVFSFCRLFLHFISFMDRTDRTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCL +YIVAAVVIYCYAGDDVTSPALGSASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMW +RHSDRMHKRDLVATGSWVLIGLATWIVAWIIAEAIPVFNNLLSLVASLFASWFTYGFSAL +FWLYLNKGRFFSTPMKTALTILNVVIMGIACCICGLGLYVSGKALHDDPSSASFSCANNA +>species2|gene0 +MGSMHEAGSRPAAGADMDTDRVHPEAVSDNERDFEKQDSKPEYQDAFGDEEYAEVKYKTL +SWCVFSAVLIVMIAVGVQRPWHGGLNATVDTNLYKAFLAVCNIVFSFCRLFLHFSSFMDR +TNKTAGHVAFFGFMAELRNPRDYPKSLFLLQGIDTCLYIIAAVVIYCYAGDDVTSPALGS +ASTIVKKVAYGIALPTIIIGGVVNGHVACKYIYVRMWRHSDRMHKRDLVATGSWVLIGLA +TWIVAWIIAEAIPVFNNLLSLVREVLVVICTMIWERVLIAPSVTAFRQPGTPDQPTEHLF +PLALFVATRDPRSIG +>species1|gene5 +MGSMLEAGSRPAADAEMDTDRVHPEAVSDGERDFEKQDSKPEYQDAFGDEEYAEVKYKTL +SWCHGCRDSVTGYSLPASGGGRLGPCPFKWAYPHIHSMGDAGEVIMGRFGRELFGTGQLL +LVVFIMASHILTFTVAMNSITDHGTCSIVFGVVGLVISFVLCLPRTLAKVSFLSVASFIS +VFSAVLIVMIAVGVQRPWHGSVNATVDTSLYKAFLAVCNIVFSFSGHVAFFGFMAELKNP +RDYPKSLFLLQGIDTCLYIVAAVVIYCYAGDDVTSPALGSASIVVKKVAYGIALPTIIIG +GVVNGHVACKYIYVRMWRHSDRMHKRDLVATGSWVLIGLATWIVAWIIAEAIPVFNNLLS +LVASLFASWFTYGFSALFWLYLNKGRFFSTPMKTALTILNVVIMGIACCICGLGLYVSGK +ALHDDPSSASFSCANNA +>species3|gene6 +MAHPTGDKVDSHLNVQTGQFFQDGREEPYLHDAEEKQDEKKGSPIYNDTFGDEEYAEVKY +KVLSWWQCGFLMVAETVSLGILSLPAVVATLGLAPAIVLIVGLGLLATYTGYVIGQFRWR +YPHVQNLADAGEILFGSIGREIFGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFG +VVGLVICFLLGLPRTSANVSYLSVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLY +EAFLAVCNIVFSFSGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGP +NVTSPALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFRHGDRMHSRDLLAT +GSWVGIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSP +RKIALTIFNVIIIGIAACICGLGLYVSGRSLHDDANGSSFSCASNA +>species0|gene2 +MAHPTGDKVDSHLNVQTGQFFQDGREEPYLHDAEEKQDEKKGSPIYNDTFGDEEYAEVKY +KVLSWWQCGFLMVAETVSLGILSLPAVVATLGLAPAIVLIVGLGLLATYTGYVIGQFRWR +YPHVQNLADAGEILFGSIGREIFGIGQLLLVIFIMASHLLTFSVAMNTITEHGTCSIVFG +VVGLVICFLLGLPRTSANVSYLSVASFISVFSAVMIVMIAVGVERPYKGTLSATVDTSLY +EAFLAVCNIVFSFSGHVAFFGFMSELKDHREYPKALCLLQGLDTILYLVTSVVIYIYAGP +NVTSPALGSASELVGKVAYGIALPTIIIGGVVNGHVACKYVYVRIFRHGDRMHSRDLLAT +GSWVGIALGLWIIAWIIAEAIPVFNDLLSLIASLFASWSTFGFSGMFWLYLNKDRLFSSP +RKIALTFFNVIIIGIAACICGLGLYVSGRSLHDDANGSSFSCASNA diff --git a/tests/samples/dataset/fake_orthologous_group_of_genes_tree.tre b/tests/samples/dataset/fake_orthologous_group_of_genes_tree.tre new file mode 100644 index 00000000..de8321a9 --- /dev/null +++ b/tests/samples/dataset/fake_orthologous_group_of_genes_tree.tre @@ -0,0 +1 @@ +(species0|gene0-duplicate_copy_0:0.00000,species0|gene0-duplicate_copy_1:0.00000,species0|gene0-duplicate_copy_2:0.00000,((((species0|gene1:0.00000,species3|gene7:0.00522)100.00:0.22839,(species1|gene2:0.01161,((species2|gene2-duplicate_copy_0:0.08052,species2|gene2-duplicate_copy_1:0.08052)100.00:0.10000,(species4|gene2-duplicate_copy_1:0.00000,species4|gene2-duplicate_copy_0:0.00000)97.00:0.00768)100.00:0.14990)100.00:0.12438)100.00:0.12438,((((((species0|gene2:0.00268,species3|gene6:0.00000)100.00:0.36783,((species1|gene5:0.05760,species2|gene0:0.17309)93.00:0.01780,species4|gene5:0.00308)100.00:0.15822)100.00:0.17836,(((species0|gene6:0.00264,species3|gene5:0.00000)100.00:0.35188,(species1|gene3:0.01222,(species2|gene3:0.04665,species4|gene3:0.01229)87.00:0.02690)100.00:0.30363)83.00:0.07673,(species2|gene1:0.03745,species4|gene6:0.02537)100.00:0.62582)67.00:0.14439)57.00:0.10412,((((species0|gene4:0.00000,species3|gene8:0.00270)100.00:0.20836,(species1|gene1:0.00567,(species2|gene6:0.03298,species4|gene4:0.00803)95.00:0.00789)99.00:0.09721)100.00:0.20351,(((species0|gene5:0.00000,species3|gene0:0.00455)100.00:0.01908,species3|gene1:0.00000)100.00:0.12662,((species1|gene4:0.00769,species4|gene0:0.00320)99.00:0.01128,species2|gene4:0.00464)100.00:0.15526)100.00:0.30301)100.00:0.22864,(species0|gene7:0.00000,species3|gene4:0.00274)100.00:0.62256)94.00:0.14833)52.00:0.09281,((species0|gene8:0.00000,species3|gene3:0.00858)100.00:0.36376,((species1|gene0:0.04145,species4|gene1:0.00956)100.00:0.09705,species2|gene5:0.02123)100.00:0.57127)55.00:0.08247)16.00:0.01681,species0|gene3:1.60327)100.00:0.29831)100.00:0.55060,species3|gene2:0.00000)100.00:0.01754)70.00:0.00000; diff --git a/tests/samples/specified_dir/OG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt b/tests/samples/specified_dir/OG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt index 7c0a48a3..57f8263d 100644 --- a/tests/samples/specified_dir/OG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt +++ b/tests/samples/specified_dir/OG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt @@ -38,3 +38,17 @@ OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CB OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 diff --git a/tests/samples/specified_dirOG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt b/tests/samples/specified_dirOG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt index ab99cf87..754364de 100644 --- a/tests/samples/specified_dirOG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt +++ b/tests/samples/specified_dirOG0000010.renamed.fa.mafft.clipkit.inparalog_report.txt @@ -14,3 +14,17 @@ OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CB OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2 +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA Aspergillus_oerlinghausenensis_CBS139183|A_oerling_CBS139183_05774-RA-duplicate +OG0000010.renamed.fa.mafft.clipkit.orthosnap.4 Aspergillus_fumigatus_Af293|EAL85095.2-duplicate Aspergillus_fumigatus_Af293|EAL85095.2