def process_fastq(fastq_r1, fastq_r2, bins, phred_offset, casava17):
fh_r1 = fastq_utils.FastQParser(fastq_r1)
fh_r2 = fastq_utils.FastQParser(fastq_r2)
oh1 = {}
oh2 = {}
root1, ext1 = os.path.splitext(fastq_r1)
root2, ext2 = os.path.splitext(fastq_r2)
for b in bins:
oh1[b] = fastq_utils.FastQWriter("%s.Q%d%s" % (root1, b, ext1))
oh2[b] = fastq_utils.FastQWriter("%s.Q%d%s" % (root2, b, ext2))
for r1 in fh_r1:
r2 = fh_r2.next()
assert fastq_utils.is_read_pair(
r1, r2, not casava17
), "FATAL: Read identifiers differ for paired reads ({:s} and {:s})".format(
r1[0], r2[0])
bin = min(int(round(fastq_utils.avgQ(r1, phred_offset))),
int(round(fastq_utils.avgQ(r2, phred_offset))))
for b in bins:
if bin >= b:
oh1[b].write(r1)
oh2[b].write(r2)
for oh in oh1.values() + oh2.values():
oh.close()
def process_fastq(fastq_r1, fastq_r2, bins, phred_offset, casava17):
fh_r1 = fastq_utils.FastQParser(fastq_r1)
fh_r2 = fastq_utils.FastQParser(fastq_r2)
oh1 = {}
oh2 = {}
root1, ext1 = os.path.splitext(fastq_r1)
root2, ext2 = os.path.splitext(fastq_r2)
for b in bins:
oh1[b] = fastq_utils.FastQWriter("%s.Q%d%s" % (root1,b,ext1))
oh2[b] = fastq_utils.FastQWriter("%s.Q%d%s" % (root2,b,ext2))
for r1 in fh_r1:
r2 = fh_r2.next()
assert fastq_utils.is_read_pair(r1,r2,not casava17), "FATAL: Read identifiers differ for paired reads ({:s} and {:s})".format(r1[0],r2[0])
bin = min(int(round(fastq_utils.avgQ(r1,phred_offset))),int(round(fastq_utils.avgQ(r2,phred_offset))))
for b in bins:
if bin >= b:
oh1[b].write(r1)
oh2[b].write(r2)
for oh in oh1.values() + oh2.values():
oh.close()
def demultiplex_fastq(index, fastq1, fastq2):
filter = {'index': index}
fp1 = FastQParser(fastq1,filter)
if fastq2 is not None:
fp2 = FastQParser(fastq2,filter)
for r1 in fp1:
if fastq2 is not None:
r2 = fp2.next()
assert is_read_pair(r1,r2), "Mismatching headers for expected read pair"
sys.stderr.write("{}\n".format("\n".join(r2)))
sys.stdout.write("{}\n".format("\n".join(r1)))
def demultiplex_fastq(index, fastq1, fastq2):
filter = {"index": index}
fp1 = FastQParser(fastq1, filter)
if fastq2 is not None:
fp2 = FastQParser(fastq2, filter)
for r1 in fp1:
if fastq2 is not None:
r2 = fp2.next()
assert is_read_pair(r1, r2), "Mismatching headers for expected read pair"
sys.stderr.write("{}\n".format("\n".join(r2)))
sys.stdout.write("{}\n".format("\n".join(r1)))
