def fastq_to_bam(fastq_files, qual_format, bam_file):
fqfhs = [parse_fastq(open(f)) for f in fastq_files]
qual_func = get_qual_conversion_func(qual_format)
header = {'HD': {'VN': '1.0', 'SO': 'unknown'}}
# 'SQ': [{'LN': 1, 'SN': 'dummy'}]}
bamfh = pysam.Samfile(bam_file, "wb", header=header)
try:
while True:
for i,fqiter in enumerate(fqfhs):
id,seq,qual = fqiter.next()
a = pysam.AlignedRead()
a.rname = -1
a.mrnm = -1
#a.pos = 0
#a.mpos = 0
a.qname = id
a.seq = seq
a.qual = qual_func(qual)
a.is_read1 = (i == 0)
a.is_read2 = (i == 1)
bamfh.write(a)
except StopIteration:
pass
bamfh.close()
def fastq_to_bam(fastq_files, qual_format, bam_file):
fqfhs = [parse_fastq(open(f)) for f in fastq_files]
qual_func = get_qual_conversion_func(qual_format)
header = {'HD': {'VN': '1.0', 'SO': 'unknown'}}
# 'SQ': [{'LN': 1, 'SN': 'dummy'}]}
bamfh = pysam.Samfile(bam_file, "wb", header=header)
try:
while True:
for i, fqiter in enumerate(fqfhs):
id, seq, qual = fqiter.next()
a = pysam.AlignedRead()
a.rname = -1
a.mrnm = -1
#a.pos = 0
#a.mpos = 0
a.qname = id
a.seq = seq
a.qual = qual_func(qual)
a.is_read1 = (i == 0)
a.is_read2 = (i == 1)
bamfh.write(a)
except StopIteration:
pass
bamfh.close()
a.mrnm = -1
#a.pos = 0
#a.mpos = 0
a.qname = id
a.seq = seq
a.qual = qual_func(qual)
a.is_read1 = (i == 0)
a.is_read2 = (i == 1)
bamfh.write(a)
except StopIteration:
pass
bamfh.close()
def bam_to_fastq(bam_file, fastq_files):
fqfhs = [open(f, "w") for f in fastq_files]
bamfh = pysam.Samfile(bam_file, "rb")
for r in bamfh:
if r.is_read1:
i = 0
elif r.is_read2:
i = 1
record = "@%s\n%s\n+\n%s" % (r.qname,r.seq,r.qual)
print >>fqfhs[i], record
if __name__ == '__main__':
sol2std = get_qual_conversion_func("solexa")
illumina2std = get_qual_conversion_func("illumina")
import sys
fastq_to_bam(["read1.fq", "read2.fq"], "solexa", "hi.bam")
bam_to_fastq("hi.bam", ["a1.fq", "a2.fq"])
#a.mpos = 0
a.qname = id
a.seq = seq
a.qual = qual_func(qual)
a.is_read1 = (i == 0)
a.is_read2 = (i == 1)
bamfh.write(a)
except StopIteration:
pass
bamfh.close()
def bam_to_fastq(bam_file, fastq_files):
fqfhs = [open(f, "w") for f in fastq_files]
bamfh = pysam.Samfile(bam_file, "rb")
for r in bamfh:
if r.is_read1:
i = 0
elif r.is_read2:
i = 1
record = "@%s\n%s\n+\n%s" % (r.qname, r.seq, r.qual)
print >> fqfhs[i], record
if __name__ == '__main__':
sol2std = get_qual_conversion_func("solexa")
illumina2std = get_qual_conversion_func("illumina")
import sys
fastq_to_bam(["read1.fq", "read2.fq"], "solexa", "hi.bam")
bam_to_fastq("hi.bam", ["a1.fq", "a2.fq"])
