class FlankingSequenceGetter(object):
def __init__(self, reffile, flanking):
self.reffile = GiantFASTAFile(reffile)
self.flanking = flanking
def get(self, chrom, pos, strand):
chromsize = self.reffile.index[chrom][0]
winleft = max(0, pos - self.flanking)
winright = min(chromsize, pos + self.flanking + 1)
leftfillsize = self.flanking - (pos - winleft)
rightfillsize = self.flanking + 1 - (winright - pos)
seq = self.reffile.get(chrom, winleft, winright, strand).upper()
if leftfillsize != 0 or rightfillsize != 0:
seq = leftfillsize * '-' + seq + rightfillsize * '-'
return seq
def __init__(self, reffile, flanking):
self.reffile = GiantFASTAFile(reffile)
self.flanking = flanking
