def doublegap_test(self): hmmaln = '...mravfiqgaeehpaafcyqvngscprtvhtlgiqlviylacaagmliivlgnvfvafavsyfkalhtptnflllslaladmflgllvlplstirsvescwffgdflcrlhtyldtlfcltsifhlcfisidrhcaicdpllypskftvrvalryilagwgvpaaytslflytdvvetrlsqwleempc' hmmaln += 'vgscqlllnk-FWG.WLNFP.L-FFVPCLIMISLYVKIFV-vatrqaqqittlskslagaakherkaaktlgiavgiyllcwlpftidtmvdsllhfitpplvfdifiwfayfnsacnpiiyvfsyqwfrkalkltlsqkvfspqtrtvdlyqe...........' aln = { 'TAAR5_HUMAN': { 5: { 'sequence': hmmaln, } } } tm_lengths = {5: 26} alignment.cut_out_aligned_part(aln, tm_lengths) seq = 'mravfiqgaeehpaafcyqvngscprtvhtlgiqlviylacaagmliivlgnvfvafavsyfkalhtptnflllslaladmflgllvlplstirsvescwffgdflcrlhtyldtlfcltsifhlcfisidrhcaicdpllypskftvrvalryilagwgvpaaytslflytdvvetrlsqwleempc' seq += 'vgscqlllnkFWGWLNFPLFFVPCLIMISLYVKIFVvatrqaqqittlskslagaakherkaaktlgiavgiyllcwlpftidtmvdsllhfitpplvfdifiwfayfnsacnpiiyvfsyqwfrkalkltlsqkvfspqtrtvdlyqe' tmseq = 'FWGWLNFPLFFVPCLIMISLYVKIFV' # TODO expected seq to contain gaps in TM section + tmseq=NKFW-GWLNF-PLFFVPCLIMISLYVKIFVV expected = { 'TAAR5_HUMAN': { 5: { 'helixseq': tmseq, 'helixlength': 26, 'sequence': seq, 'seqlength': 337, 'firstaa': 198, 'lastaa': 224, 'cut_off': True } } } self.maxDiff = None self.assertEquals(aln, expected)
def nogaps_test(self): hmmaln = '................................................................' hmmaln += '....................menetvselnqtqlqpravvaleyqvvtillvliicglgivgn' hmmaln += 'imvvlvvmrtkhmrtptncylvslavadlmvlvaaglpnitdsiygswvygyvGCLCITYL.Q' hmmaln += '.YLGIN.A..SSCSI.T..AFTIERYIAichpikaqflctfsrakkiiifvwaftslycmlwf' hmmaln += 'flldlnistykdaiviscgykisrnyyspiylmdfgvfyvvpmilatvlygfiarilflnpip' hmmaln += 'sdpkensktwkndsthqntnlnvntsnrcfnstvssrkqvtkmlavvvilfallwmpyrtlvv' hmmaln += 'vnsflsspfqenwfllfcriciylnsainpviynlmsqkfraafrklcnckqkptekpanysv' hmmaln += 'alnysvikesdhfsteldditvtdtylsatkvsfddtclasevsfsqs.........' aln = { 'TRFR_HUMAN': { 3: { 'sequence': hmmaln, } } } tm_lengths = {3: 30} alignment.cut_out_aligned_part(aln, tm_lengths) seq = 'menetvselnqtqlqpravvaleyqvvtillvliicglgivgn' seq += 'imvvlvvmrtkhmrtptncylvslavadlmvlvaaglpnitdsiygswvygyvGCLCITYLQ' seq += 'YLGINASSCSITAFTIERYIAichpikaqflctfsrakkiiifvwaftslycmlwf' seq += 'flldlnistykdaiviscgykisrnyyspiylmdfgvfyvvpmilatvlygfiarilflnpip' seq += 'sdpkensktwkndsthqntnlnvntsnrcfnstvssrkqvtkmlavvvilfallwmpyrtlvv' seq += 'vnsflsspfqenwfllfcriciylnsainpviynlmsqkfraafrklcnckqkptekpanysv' seq += 'alnysvikesdhfsteldditvtdtylsatkvsfddtclasevsfsqs' tmseq = 'GCLCITYLQYLGINASSCSITAFTIERYIA' expected = { 'TRFR_HUMAN': { 3: { 'helixseq': tmseq, 'helixlength': 30, 'sequence': seq, 'seqlength': 398, 'firstaa': 96, 'lastaa': 126, 'cut_off': True } } } self.assertEquals(aln, expected)
def singlegap_test(self): hmmaln = '...mdgsnvtsfvveeptnistgrnasvgnahrqipivhwvimsispvgfvengillwflcfrmrrnpft-VYITHLSIA..DISLLF..CIFILSI--dya' hmmaln += 'ldyelssghyytivtlsvtflfgyntglylltaisverclsvlypiwyrchrpkyqsalvcallwalsclvttmeyvmcidreeeshsrndcraviifiailsflvftplmlvsstilvvkirkntwashssklyivimvtiiiflifampmrllyllyyeywstfgnlhhisllfstinssanpfiyffvgsskkkrfk' hmmaln += 'eslkvvltrafkdemqprrqkdncntvtvetvv.......................................................................................................................................................................' aln = { 'MAS_HUMAN': { 2: { 'sequence': hmmaln, } } } tm_lengths = {2: 26} alignment.cut_out_aligned_part(aln, tm_lengths) seq = 'mdgsnvtsfvveeptnistgrnasvgnahrqipivhwvimsispvgfvengillwflcfrmrrnpftVYITHLSIADISLLFCIFILSIdya' seq += 'ldyelssghyytivtlsvtflfgyntglylltaisverclsvlypiwyrchrpkyqsalvcallwalsclvttmeyvmcidreeeshsrndcraviifiailsflvftplmlvsstilvvkirkntwashssklyivimvtiiiflifampmrllyllyyeywstfgnlhhisllfstinssanpfiyffvgsskkkrfk' seq += 'eslkvvltrafkdemqprrqkdncntvtvetvv' tmseq = 'VYITHLSIADISLLFCIFILSI' # TODO expected seq to contain gaps in TM section + tmseq=TVYITHLSIADISLLF-CIFILSIDY expected = { 'MAS_HUMAN': { 2: { 'helixseq': tmseq, 'helixlength': 22, 'sequence': seq, 'seqlength': 325, 'firstaa': 67, 'lastaa': 89, 'cut_off': True } } } self.maxDiff = None self.assertEquals(aln, expected)