motif2 = motility.IUPAC('RGWYV')
winTo2ndMotif = (23,27) # <---- This is based from END of first motif!!!
seqList = zipped = zip(seqFile[:-1:2], seqFile[1::2])
seqDict = {}
print 'populating seqDict...'
for item in seqList:
name = item[0].replace('|Inr(..DPE)','').replace('>','')
header = item[0]
seq = item[1]
coverage = item[0].split('|')[-1].split('-')
coverage = (int(coverage[0]),int(coverage[1]))
motif1Loc = coverage[0]-6
seqDict[name] = DNAseq(seq,name,header)
seqDict[name].coverage = coverage
seqDict[name].motif1Loc = motif1Loc
def checkSlice(seqObj, motif2, winTo2ndMotif):
motif2Loc = None
mHits = motif2.find(seqObj.toString())
for each in mHits:
if each[2] == -1:
continue
elif each[0] >= winTo2ndMotif[0] and each[0]<= winTo2ndMotif[1]:
motif2Loc = each[0]
if motif2Loc:
return '%s\t%s\t%s\t%s\n' % (seqObj.name,seqObj.motif1Loc,motif2Loc+seqObj.coverage[0],motif2Loc)
else:
