def write_pair_fastq(fastq_file1, fastq_file2, orig_read1, orig_read2,
new_pairs):
n_pair = len(new_pairs)
i = 1
for pair in new_pairs:
# give each fastq record a new name giving:
# 1 - the original name of the read
# 2 - the coordinates the two ends of the pair should map to
# 3 - the number of the read
# 4 - the total number of reads being remapped
pos_str = "%d-%d" % (min(orig_read1.pos + 1, orig_read2.pos + 1),
max(orig_read1.pos + 1, orig_read2.pos + 1))
name = "%s.%s.%d.%d" % (orig_read1.qname, pos_str, i, n_pair)
fastq_file1.write("@%s\n%s\n+%s\n%s\n" %
(name, pair[0], name, orig_read1.qual))
rev_seq = util.revcomp(pair[1])
fastq_file2.write("@%s\n%s\n+%s\n%s\n" %
(name, rev_seq, name, orig_read2.qual))
i += 1
def write_pair_fastq(fastq_file1, fastq_file2, orig_read1, orig_read2,
new_pairs):
n_pair = len(new_pairs)
i = 1
for pair in new_pairs:
# give each fastq record a new name giving:
# 1 - the original name of the read
# 2 - the coordinates the two ends of the pair should map to
# 3 - the number of the read
# 4 - the total number of reads being remapped
pos_str = "%d-%d" % (min(orig_read1.pos+1, orig_read2.pos+1),
max(orig_read1.pos+1, orig_read2.pos+1))
name = "%s.%s.%d.%d" % (orig_read1.qname, pos_str, i, n_pair)
fastq_file1.write("@%s\n%s\n+%s\n%s\n" %
(name, pair[0], name, orig_read1.qual))
rev_seq = util.revcomp(pair[1])
fastq_file2.write("@%s\n%s\n+%s\n%s\n" %
(name, rev_seq, name, orig_read2.qual))
i += 1
def write_pair_fastq(fastq_file1, fastq_file2, orig_read1, orig_read2,
new_pairs, files):
# create new names for new reads keeping track of chromosome and matched position of original read
# give each fastq record a new name giving:
# 1 - the original name of the read
# 2 - the chrom the reads should map
# 3 - the coordinates the two ends of the pair should map to
pos_str = "%d-%d" % (min(orig_read1.pos + 1, orig_read2.pos + 1),
max(orig_read1.pos + 1, orig_read2.pos + 1))
name = "%s.%s.%s" % (orig_read1.qname, orig_read1.reference_name, pos_str)
## save original and new reads
## check which read neads to be reversed
if orig_read1.is_reverse:
rev = util.revcomp(orig_read1.seq)
rev_q = orig_read1.qual[::-1]
fastq_file1.write("@%s\n%s\n+%s\n%s\n" %
(orig_read1.qname, rev, orig_read1.qname, rev_q))
fastq_file2.write("@%s\n%s\n+%s\n%s\n" %
(orig_read2.qname, orig_read2.seq, orig_read2.qname,
orig_read2.qual))
rev_seq = util.revcomp(new_pairs[0])
fastq_file1.write("@%s\n%s\n+%s\n%s\n" % (name, rev_seq, name, rev_q))
fastq_file2.write("@%s\n%s\n+%s\n%s\n" %
(name, new_pairs[1], name, orig_read2.qual))
else:
rev = util.revcomp(orig_read2.seq)
rev_q = orig_read2.qual[::-1]
fastq_file1.write("@%s\n%s\n+%s\n%s\n" %
(orig_read1.qname, orig_read1.seq, orig_read1.qname,
orig_read1.qual))
fastq_file2.write("@%s\n%s\n+%s\n%s\n" %
(orig_read2.qname, rev, orig_read2.qname, rev_q))
rev_seq = util.revcomp(new_pairs[1])
fastq_file1.write("@%s\n%s\n+%s\n%s\n" %
(name, new_pairs[0], name, orig_read1.qual))
fastq_file2.write("@%s\n%s\n+%s\n%s\n" % (name, rev_seq, name, rev_q))