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 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 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)
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)