def fastq_to_dict(fastq):
"""docstring for fastq_to_dict"""
d = {}
with nopen(fastq) as fh:
for name, seq, qual in read_fastx(fh):
d[name] = {'seq':seq,'qual':qual}
return d
def main(args):
for fastq in args.fastq:
print fastq
meta = Counter()
with nopen(fastq) as fh:
for name, seq, qual in read_fastx(fh):
name, cregion, fwork = name.split()[0].split(":")
meta.update(["%s:%s" % (cregion, fwork)])
for combination, count in meta.iteritems():
print "%s\t%d" % (combination, count)
def fq_to_set(fq):
fq_l = []
fq_d = {}
with nopen(fq) as fh:
for name, seq, qual in read_fastx(fh):
# split name on whitespace, leaving off "1" or "2"
read_id = name.split()[0]
fq_l.append(read_id)
# a million reads ~ 1 GB
fq_d[read_id] = "@%s\n%s\n+\n%s\n" % (name, seq, qual)
return set(fq_l), fq_d
