def postProcessOutput(self):
super(BlastOutput6ParserAnalysis,self).postProcessOutput()
data = {}
file = self.input_files[0]
with open(file) as fp:
for line in fp:
line = line.rstrip('\n')
ff = line.split('\t')
qid = ff[0]
hid = ff[1]
pid = float(ff[2])
alnlen = ff[3]
mm = int(ff[4])
gaps = int(ff[5])
qstart = int(ff[6])
qend = int(ff[7])
hstart = int(ff[8])
hend = int(ff[9])
exval = float(ff[10])
score = float(ff[11])
feat = Feature()
feat.qid = qid
feat.qstart = qstart
feat.qend = qend
feat.hid = hid
feat.hstart = hstart
feat.hend = hend
feat.pid = pid
feat.score = score
feat.mm = mm
feat.gaps = gaps
feat.exval = exval
if len(ff) > 12:
feat.qlen = int(ff[12])
feat.hlen = int(ff[13])
feat.qseq = ff[14]
feat.hseq = ff[15]
if not qid in data:
data[qid] = []
tmp = data[qid]
tmp.append(feat)
self.data = data
def parseBlastOutput6(file):
hits = {}
prev = None
with open(file) as fp:
for line in fp:
line = line.rstrip('\n')
ff = line.split('\t')
qid = ff[0]
hid = ff[1]
pid = float(ff[2])
alnlen = ff[3]
mm = int(ff[4])
gaps = int(ff[5])
qstart = int(ff[6])
qend = int(ff[7])
hstart = int(ff[8])
hend = int(ff[9])
exval = float(ff[10])
score = float(ff[11])
feat = Feature()
feat.qid = qid
feat.qstart = qstart
feat.qend = qend
feat.hid = hid
feat.hstart = hstart
feat.hend = hend
feat.pid = pid
feat.score = score
feat.mm = mm
feat.gaps = gaps
feat.exval = exval
if len(ff) > 15:
feat.qlen = int(ff[12])
feat.hlen = int(ff[13])
feat.qseq = ff[14]
feat.hseq = ff[15]
if not qid in hits:
hits[qid] = []
tmp = hits[qid]
tmp.append(feat)
return hits