def seq_waytoosmall_alnextended_test(self):
seq = 'MENETVSELNQTQLQPRAVVALEYQVVTILLVLIICGLGIVGNIMVVLVVMRTKHMRTPT'
seq += 'NCYLVSLAVADLMVLVAAGLPNITDSIYGSWVYGYVGCLCITYLQYLGINASSCSITAFT'
seq += 'IERYIAICHPIKAQFLCTFSRAKKIIIFVWAFTSLYCMLWFFLLDLNISTYKDAIVISCG'
seq += 'YKISRNYYSPIYLMDFGVFYVVPMILATVLYGFIARILFLNPIPSDPKENSKTWKNDSTH'
seq += 'QNTNLNVNTSNRCFNSTVSSRKQVTKMLAVVVILFALLWMPYRTLVVVNSFLSSPFQENW'
seq += 'FLLFCRICIYLNSAINPVIYNLMSQKFRAAFRKLCNCKQKPTEKPANYSVALNYSVIKES'
seq += 'DHFSTELDDITVTDTYLSATKVSFDDTCLASEVSFSQS'
tmseq = 'QYLGINASSCSI'
aln = {
'TRFR_HUMAN': {
3: {
'helixseq': tmseq,
'sequence': seq,
'firstaa': 104,
'lastaa': 116
}
}
}
tms = {3: 30}
preferred_gaps = {3: []}
alignment.fix_wrong_lengths(aln, tms, self.score_matrix, preferred_gaps)
expected_seq = 'GCLCITYLQYLGINASSCSITAFTIERYIA'
self.assertEquals(aln['TRFR_HUMAN'][3]['helixseq'], expected_seq)
self.assertEquals(aln['TRFR_HUMAN'][3]['firstaa'], 96)
self.assertEquals(aln['TRFR_HUMAN'][3]['lastaa'], 126)
def seq_waytoosmall_alnextended_test(self):
seq = 'MENETVSELNQTQLQPRAVVALEYQVVTILLVLIICGLGIVGNIMVVLVVMRTKHMRTPT'
seq += 'NCYLVSLAVADLMVLVAAGLPNITDSIYGSWVYGYVGCLCITYLQYLGINASSCSITAFT'
seq += 'IERYIAICHPIKAQFLCTFSRAKKIIIFVWAFTSLYCMLWFFLLDLNISTYKDAIVISCG'
seq += 'YKISRNYYSPIYLMDFGVFYVVPMILATVLYGFIARILFLNPIPSDPKENSKTWKNDSTH'
seq += 'QNTNLNVNTSNRCFNSTVSSRKQVTKMLAVVVILFALLWMPYRTLVVVNSFLSSPFQENW'
seq += 'FLLFCRICIYLNSAINPVIYNLMSQKFRAAFRKLCNCKQKPTEKPANYSVALNYSVIKES'
seq += 'DHFSTELDDITVTDTYLSATKVSFDDTCLASEVSFSQS'
tmseq = 'QYLGINASSCSI'
aln = {
'TRFR_HUMAN': {
3: {
'helixseq': tmseq,
'sequence': seq,
'firstaa': 104,
'lastaa': 116
}
}
}
tms = {3: 30}
preferred_gaps = {3: []}
alignment.fix_wrong_lengths(aln, tms, self.score_matrix,
preferred_gaps)
expected_seq = 'GCLCITYLQYLGINASSCSITAFTIERYIA'
self.assertEquals(aln['TRFR_HUMAN'][3]['helixseq'], expected_seq)
self.assertEquals(aln['TRFR_HUMAN'][3]['firstaa'], 96)
self.assertEquals(aln['TRFR_HUMAN'][3]['lastaa'], 126)
def add_preferred_gaps_test(self):
seq = 'MAPWPHENSSLAPWPDLPTLAPNTANTSGLPGVPWEAALAGALLALAVLATVGGNLLVIV'
seq += 'AIAWTPRLQTMTNVFVTSLAAADLVMGLLVVPPAATLALTGHWPLGATGCELWTSVDVLC'
seq += 'VTASIETLCALAVDRYLAVTNPLRYGALVTKRCARTAVVLVWVVSAAVSFAPIMSQWWRV'
seq += 'GADAEAQRCHSNPRCCAFASNMPYVLLSSSVSFYLPLLVMLFVYARVFVVATRQLRLLRG'
seq += 'ELGRFPPEESPPAPSRSLAPAPVGTCAPPEGVPACGRRPARLLPLREHRALCTLGLIMGT'
seq += 'FTLCWLPFFLANVLRALGGPSLVPGPAFLALNWLGYANSAFNPLIYCRSPDFRSAFRRLL'
seq += 'CRCGRRLPPEPCAAARPALFPSGVPAARSSPAQPRLCQRLDGASWGVS'
tmseq = 'YVLLSSSVSFYLPLLVMLFVYARVFV'
aln = {
'ADRB3_HUMAN': {
5: {
'helixseq': tmseq,
'sequence': seq,
'firstaa': 203,
'lastaa': 229
}
}
}
tms = {5: 31}
preferred_gaps = {5: [5, 11]}
alignment.fix_wrong_lengths(aln, tms, self.score_matrix, preferred_gaps)
expected_seq = 'MPYV-LLSSS-VSFYLPLLVMLFVYARVFVV'
self.assertEquals(aln['ADRB3_HUMAN'][5]['helixseq'], expected_seq)
self.assertEquals(aln['ADRB3_HUMAN'][5]['firstaa'], 201)
self.assertEquals(aln['ADRB3_HUMAN'][5]['lastaa'], 230)
def add_preferred_gaps_test(self):
seq = 'MAPWPHENSSLAPWPDLPTLAPNTANTSGLPGVPWEAALAGALLALAVLATVGGNLLVIV'
seq += 'AIAWTPRLQTMTNVFVTSLAAADLVMGLLVVPPAATLALTGHWPLGATGCELWTSVDVLC'
seq += 'VTASIETLCALAVDRYLAVTNPLRYGALVTKRCARTAVVLVWVVSAAVSFAPIMSQWWRV'
seq += 'GADAEAQRCHSNPRCCAFASNMPYVLLSSSVSFYLPLLVMLFVYARVFVVATRQLRLLRG'
seq += 'ELGRFPPEESPPAPSRSLAPAPVGTCAPPEGVPACGRRPARLLPLREHRALCTLGLIMGT'
seq += 'FTLCWLPFFLANVLRALGGPSLVPGPAFLALNWLGYANSAFNPLIYCRSPDFRSAFRRLL'
seq += 'CRCGRRLPPEPCAAARPALFPSGVPAARSSPAQPRLCQRLDGASWGVS'
tmseq = 'YVLLSSSVSFYLPLLVMLFVYARVFV'
aln = {
'ADRB3_HUMAN': {
5: {
'helixseq': tmseq,
'sequence': seq,
'firstaa': 203,
'lastaa': 229
}
}
}
tms = {5: 31}
preferred_gaps = {5: [5, 11]}
alignment.fix_wrong_lengths(aln, tms, self.score_matrix,
preferred_gaps)
expected_seq = 'MPYV-LLSSS-VSFYLPLLVMLFVYARVFVV'
self.assertEquals(aln['ADRB3_HUMAN'][5]['helixseq'], expected_seq)
self.assertEquals(aln['ADRB3_HUMAN'][5]['firstaa'], 201)
self.assertEquals(aln['ADRB3_HUMAN'][5]['lastaa'], 230)
