def _parse_csfasta_with_qual(csfasta, qual):
ffh = seek_to_start(csfasta)
qfh = seek_to_start(qual)
for fasta, qual in izip(ffh, qfh):
fasta = fasta.strip()
fnew = fasta.startswith(">")
qual = qual.strip()
qnew = qual.startswith(">")
if fnew ^ qnew: # xor
raise Exception("Mismatched files: id and info not aligned")
elif fnew and qnew:
fid = fasta[1:]
qid = qual[1:]
if fid != qid:
raise Exception("Mismatched files: id's do not match")
# record = {'id' : fid, 'sequence' : None, 'quality' : None}
record = SolidRead(fid)
else:
record.sequence = fasta
record.quality = qual
yield record
ffh.close()
qfh.close()
raise StopIteration("Parsing finished")
def _parse_csfasta_with_qual(csfasta, qual):
ffh = seek_to_start(csfasta)
qfh = seek_to_start(qual)
for fasta,qual in izip(ffh, qfh):
fasta = fasta.strip()
fnew = fasta.startswith(">")
qual = qual.strip()
qnew = qual.startswith(">")
if fnew ^ qnew: # xor
raise Exception("Mismatched files: id and info not aligned")
elif fnew and qnew:
fid = fasta[1:]
qid = qual[1:]
if fid != qid:
raise Exception("Mismatched files: id's do not match")
# record = {'id' : fid, 'sequence' : None, 'quality' : None}
record = SolidRead(fid)
else:
record.sequence = fasta
record.quality = qual
yield record
ffh.close()
qfh.close()
raise StopIteration("Parsing finished")
def _parse_csfasta_only(csfasta):
ffh = seek_to_start(csfasta)
for fasta in ffh:
fasta = fasta.strip()
fnew = fasta.startswith(">")
if fnew:
fid = fasta[1:]
# record = {'id' : fid, 'sequence' : None, 'quality' : None}
record = SolidRead(fid)
else:
record.sequence = fasta
yield record
ffh.close()
raise StopIteration("Parsing finished")
def _parse_csfasta_only(csfasta):
ffh = seek_to_start(csfasta)
for fasta in ffh:
fasta = fasta.strip()
fnew = fasta.startswith(">")
if fnew:
fid = fasta[1:]
# record = {'id' : fid, 'sequence' : None, 'quality' : None}
record = SolidRead(fid)
else:
record.sequence = fasta
yield record
ffh.close()
raise StopIteration("Parsing finished")
