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added parsing of FASTA/FASTQ comment (everything after space) #6

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added parsing of FASTA/FASTQ comment (everything after space) #6

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11 changes: 6 additions & 5 deletions readfq.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,15 @@ def readfq(fp): # this is a generator function
last = l[:-1] # save this line
break
if not last: break
name, seqs, last = last[1:].partition(" ")[0], [], None
name, _, comment = last[1:].partition(" ")
seqs, last = [], None
for l in fp: # read the sequence
if l[0] in '@+>':
last = l[:-1]
break
seqs.append(l[:-1])
if not last or last[0] != '+': # this is a fasta record
yield name, ''.join(seqs), None # yield a fasta record
yield name, comment, ''.join(seqs), None # yield a fasta record
if not last: break
else: # this is a fastq record
seq, leng, seqs = ''.join(seqs), 0, []
Expand All @@ -23,16 +24,16 @@ def readfq(fp): # this is a generator function
leng += len(l) - 1
if leng >= len(seq): # have read enough quality
last = None
yield name, seq, ''.join(seqs); # yield a fastq record
yield name, comment, seq, ''.join(seqs); # yield a fastq record
break
if last: # reach EOF before reading enough quality
yield name, seq, None # yield a fasta record instead
yield name, comment, seq, None # yield a fasta record instead
break

if __name__ == "__main__":
import sys
n, slen, qlen = 0, 0, 0
for name, seq, qual in readfq(sys.stdin):
for name, comment, seq, qual in readfq(sys.stdin):
n += 1
slen += len(seq)
qlen += qual and len(qual) or 0
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