def getSequence(self, blastDb, padFivePrime=0, padThreePrime=0):
if self.genomic:
start = max(1,self.sStart-padFivePrime)
end = self.sEnd+padThreePrime
h,s = blast.getSequence(blastDb, self.accession, start, end, self.strand)
else:
raise Exception('You must call the toGenomic method first.')
return h,s
def getSequence(self, blastDb, padFivePrime=0, padThreePrime=0):
if self.genomic:
start = max(1, self.sStart - padFivePrime)
end = self.sEnd + padThreePrime
h, s = blast.getSequence(blastDb, self.accession, start, end,
self.strand)
else:
raise Exception('You must call the toGenomic method first.')
return h, s
def getSequence(self, blastdb, getAll=False, convertAccession=lambda x: x):
if getAll:
start = 0
end = 0
else:
start = self.sStart
end = self.sEnd
accession = convertAccession(self.accession)
h, s = blast.getSequence(blastdb, accession, start, end)
return h, s
def getSequence(self, blastdb, getAll=False, convertAccession=lambda x: x):
if getAll:
start = 0
end = 0
else:
start = self.sStart
end = self.sEnd
accession = convertAccession(self.accession)
h,s = blast.getSequence(blastdb, accession, start, end)
return h,s
def getSequence(self, blastDb, padFivePrime=0, padThreePrime=0):
start = max(1, self.sStart - padFivePrime)
end = self.sEnd + padThreePrime
h, s = blast.getSequence(blastDb, self.accession, start, end,
self.strand)
return h, s
def getSequence(self, blastDb, padFivePrime=0, padThreePrime=0):
start = max(1,self.sStart-padFivePrime)
end = self.sEnd+padThreePrime
h,s = blast.getSequence(blastDb, self.accession, start, end, self.strand)
return h,s