def convert_colorspace(color_seq, char_a, char_b):
"""
take a colorspace read, convert to base sequence
convert C to T (char_a to char_b) then back to
colorspace and return
"""
base_seq = cs2seq(color_seq.rstrip()).replace(char_a, char_b)
return seq2cs(base_seq)
def convert_colorspace(color_seq, char_a, char_b):
"""
take a colorspace read, convert to base sequence
convert C to T (char_a to char_b) then back to
colorspace and return
"""
base_seq = cs2seq(color_seq.rstrip()).replace(char_a, char_b)
return seq2cs(base_seq)
def parse_sam(sam_iter, chr_lengths, get_records, unmapped_name,
is_colorspace, out_sam):
is_colorspace = int(is_colorspace)
unmapped = open(unmapped_name, "w")
print >>sys.stderr, "writing unmapped reads to %s" % (unmapped.name, )
idx = 0
write_new_header(out_sam, chr_lengths)
for sline in sam_iter:
# comment.
if sline[0] == "@":
copy_header(out_sam, sline, chr_lengths)
continue
line = sline.split("\t")
read_id = line[0]
sam_flag = int(line[1])
# no reported alignments.
# extra via -m
if sam_flag == 4:
if not "XM:i:0" in sline:
# write stuff that was excluded because of too many mappings.
raw_fastq, converted_fastq = get_records(read_id, 0)
print >> unmapped, str(raw_fastq)
continue
# extra found via -M
if line[4] == '0' and sam_flag == 0:
raw_fastq, converted_fastq = get_records(read_id, 0)
print >> unmapped, str(raw_fastq)
continue
if sam_flag != 0:
# if the pair doesn't map to same place, skip.
if line[6] != "=": continue
# flags are (1 | 2 | 32 | 64) or (1 | 2 | 16 | 128)
idx = 0 if (sam_flag & 128) == 0 else 1
# bowtie prints the alignment without the pair end info.
# add back /0 or /1 here.
read_id = read_id + "/" + str(idx + 1)
seqid = line[2]
direction = seqid[0]
assert direction in 'fr'
seqid = seqid[1:]
line[2] = seqid
pos0 = int(line[3]) - 1
if is_colorspace: pos0 -= 2
converted_seq = line[9]
# we want to include the orginal, non converted reads
# in the output file to view the alignment.
# read_id is the line in the file.
#fh_raw_reads.seek((read_id * read_len) + read_id)
#raw_seq = fh_raw_reads.read(read_len)
raw_fastq, converted_fastq = get_records(read_id, idx)
read_len = len(converted_seq) + 3 * int(is_colorspace)
raw_seq = raw_fastq.seq
if is_colorspace:
raw_seq = cs2seq(raw_seq)
if direction == 'f':
line[9] = raw_seq
else:
pos0 = chr_lengths[seqid] - pos0 - read_len
# adjust mate position as well.
mpos = int(line[7])
mpos = chr_lengths[seqid] - mpos - read_len + 2
line[8] = str(pos0 - mpos + 1) # insert size
line[7] = str(mpos)
line[3] = str(pos0 + 1)
# since the read matched the flipped genome. we flip it here.
line[9] = raw_seq = revcomp(raw_seq)
# flip the quality as well.
line[10] = line[10][::-1]
line[1] = str(sam_flag + 16) # alignment on reverse strand.
converted_seq = revcomp(converted_fastq.seq)
if (sam_flag & 128 != 0): # th other end of the pair.
line[9] = raw_seq = revcomp(raw_seq)
converted_seq = revcomp(converted_seq)
# NM:i:2
NM = [x for x in line[11:] if x[0] == 'N' and x[1] == 'M'][0].rstrip()
nmiss = int(NM[-1])
line[-1] = line[-1].rstrip()
yield dict(
read_id=read_id,
seqid=line[2],
pos0=pos0,
mapq=line[4],
nmiss=nmiss,
read_sequence=converted_seq,
raw_read=raw_seq,
), line, read_len, direction
def parse_sam(sam_iter, chr_lengths, get_records, unmapped_name, is_colorspace,
out_sam):
is_colorspace = int(is_colorspace)
unmapped = open(unmapped_name, "w")
print >> sys.stderr, "writing unmapped reads to %s" % (unmapped.name, )
idx = 0
write_new_header(out_sam, chr_lengths)
for sline in sam_iter:
# comment.
if sline[0] == "@":
copy_header(out_sam, sline, chr_lengths)
continue
line = sline.split("\t")
read_id = line[0]
sam_flag = int(line[1])
# no reported alignments.
# extra via -m
if sam_flag == 4:
if not "XM:i:0" in sline:
# write stuff that was excluded because of too many mappings.
raw_fastq, converted_fastq = get_records(read_id, 0)
print >> unmapped, str(raw_fastq)
continue
# extra found via -M
if line[4] == '0' and sam_flag == 0:
raw_fastq, converted_fastq = get_records(read_id, 0)
print >> unmapped, str(raw_fastq)
continue
if sam_flag != 0:
# if the pair doesn't map to same place, skip.
if line[6] != "=": continue
# flags are (1 | 2 | 32 | 64) or (1 | 2 | 16 | 128)
idx = 0 if (sam_flag & 128) == 0 else 1
# bowtie prints the alignment without the pair end info.
# add back /0 or /1 here.
read_id = read_id + "/" + str(idx + 1)
seqid = line[2]
direction = seqid[0]
assert direction in 'fr'
seqid = seqid[1:]
line[2] = seqid
pos0 = int(line[3]) - 1
if is_colorspace: pos0 -= 2
converted_seq = line[9]
# we want to include the orginal, non converted reads
# in the output file to view the alignment.
# read_id is the line in the file.
#fh_raw_reads.seek((read_id * read_len) + read_id)
#raw_seq = fh_raw_reads.read(read_len)
raw_fastq, converted_fastq = get_records(read_id, idx)
read_len = len(converted_seq) + 3 * int(is_colorspace)
raw_seq = raw_fastq.seq
if is_colorspace:
raw_seq = cs2seq(raw_seq)
if direction == 'f':
line[9] = raw_seq
else:
pos0 = chr_lengths[seqid] - pos0 - read_len
# adjust mate position as well.
mpos = int(line[7])
mpos = chr_lengths[seqid] - mpos - read_len + 2
line[8] = str(pos0 - mpos + 1) # insert size
line[7] = str(mpos)
line[3] = str(pos0 + 1)
# since the read matched the flipped genome. we flip it here.
line[9] = raw_seq = revcomp(raw_seq)
# flip the quality as well.
line[10] = line[10][::-1]
line[1] = str(sam_flag + 16) # alignment on reverse strand.
converted_seq = revcomp(converted_fastq.seq)
if (sam_flag & 128 != 0): # th other end of the pair.
line[9] = raw_seq = revcomp(raw_seq)
converted_seq = revcomp(converted_seq)
# NM:i:2
NM = [x for x in line[11:] if x[0] == 'N' and x[1] == 'M'][0].rstrip()
nmiss = int(NM[-1])
line[-1] = line[-1].rstrip()
yield dict(
read_id=read_id,
seqid=line[2],
pos0=pos0,
mapq=line[4],
nmiss=nmiss,
read_sequence=converted_seq,
raw_read=raw_seq,
), line, read_len, direction
