def bam_innerdist(bam1, bam2, summaryout=None):
iter1 = bam_iter(bam1)
iter2 = bam_iter(bam2, quiet=True)
distances = {}
total = 0
proper = 0
orientation_count = {"+/-": 0, "-/+": 0, "+/+": 0, "-/-": 0}
read1_last = None
read2_last = None
read1 = None
read2 = None
while True:
try:
while not read1 or read1_last == read1.qname:
read1 = iter1.next()
while not read2 or read2_last == read2.qname:
read2 = iter2.next()
except StopIteration:
break
if read1.qname != read2.qname:
raise ValueError("Error: BAM files aren't properly paired! (%s, %s)\n" % (read1.qname, read2.qname))
read1_last = read1.qname
read2_last = read2.qname
total += 1
if read1.is_unmapped or read2.is_unmapped or read1.tid != read2.tid:
continue
proper += 1
if read1.pos < read2.pos:
dist = read2.pos - read1.aend
else:
dist = read1.pos - read2.aend
if summaryout:
summaryout.write("%s\n" % dist)
if not dist in distances:
distances[dist] = 1
else:
distances[dist] += 1
orientation = "%s/%s" % ("-" if read1.is_reverse else "+", "-" if read2.is_reverse else "+")
orientation_count[orientation] += 1
mean, stdev = counts_mean_stdev(distances)
return total, proper, mean, stdev, orientation_count
def bam_renamepair(infile, outfile, delim='/'):
bam = pysam.Samfile(infile, "rb")
out = pysam.Samfile(outfile, "wb", template=bam)
for read in bam_iter(bam):
read_renamepair(read, delim)
out.write(read)
bam.close()
out.close()
def bam_renamepair(infile, outfile, delim='/'):
bam = pysam.Samfile(infile, "rb")
out = pysam.Samfile(outfile, "wb", template=bam)
for read in bam_iter(bam):
read_renamepair(read, delim)
out.write(read)
bam.close()
out.close()
def bam_filter(infile, outfile, criteria, failedfile=None, verbose=False):
if verbose:
sys.stderr.write('Input file : %s\n' % infile)
sys.stderr.write('Output file : %s\n' % outfile)
if failedfile:
sys.stderr.write('Failed reads: %s\n' % failedfile)
sys.stderr.write('Criteria:\n')
for criterion in criteria:
sys.stderr.write(' %s\n' % criterion)
sys.stderr.write('\n')
bamfile = pysam.Samfile(infile, "rb")
outfile = pysam.Samfile(outfile, "wb", template=bamfile)
if failedfile:
failed_out = open(failedfile, 'w')
else:
failed_out = None
passed = 0
failed = 0
def _callback(read):
return "%s | %s kept,%s failed" % ('%s:%s' % (bamfile.getrname(
read.tid), read.pos) if read.tid > -1 else 'unk', passed, failed)
for read in bam_iter(bamfile, quiet=True):
p = True
for criterion in criteria:
if not criterion.filter(bamfile, read):
p = False
failed += 1
if failed_out:
failed_out.write('%s\t%s\n' % (read.qname, criterion))
# outfile.write(read_to_unmapped(read))
break
if p:
passed += 1
outfile.write(read)
bamfile.close()
outfile.close()
if failed_out:
failed_out.close()
sys.stdout.write("%s kept\n%s failed\n" % (passed, failed))
for criterion in criteria:
criterion.close()
def bam_export(bam, mapped=True, unmapped=True, whitelist=None, blacklist=None, fields=None, out=sys.stdout, quiet=False):
for read in bam_iter(bam, quiet=quiet):
if whitelist and not read.qname in whitelist:
continue
if blacklist and read.qname in blacklist:
continue
try:
if mapped and not read.is_unmapped:
export_read(bam, read, fields, out)
elif unmapped and read.is_unmapped:
export_read(bam, read, fields, out)
except IOError:
break
def bam_filter(infile, outfile, criteria, failedfile=None, verbose=False):
if verbose:
sys.stderr.write('Input file : %s\n' % infile)
sys.stderr.write('Output file : %s\n' % outfile)
if failedfile:
sys.stderr.write('Failed reads: %s\n' % failedfile)
sys.stderr.write('Criteria:\n')
for criterion in criteria:
sys.stderr.write(' %s\n' % criterion)
sys.stderr.write('\n')
bamfile = pysam.Samfile(infile, "rb")
outfile = pysam.Samfile(outfile, "wb", template=bamfile)
if failedfile:
failed_out = open(failedfile, 'w')
else:
failed_out = None
passed = 0
failed = 0
def _callback(read):
return "%s | %s kept,%s failed" % ('%s:%s' % (bamfile.getrname(read.tid), read.pos) if read.tid > -1 else 'unk', passed, failed)
for read in bam_iter(bamfile, quiet=True):
p = True
for criterion in criteria:
if not criterion.filter(bamfile, read):
p = False
failed += 1
if failed_out:
failed_out.write('%s\t%s\n' % (read.qname, criterion))
# outfile.write(read_to_unmapped(read))
break
if p:
passed += 1
outfile.write(read)
bamfile.close()
outfile.close()
if failed_out:
failed_out.close()
sys.stdout.write("%s kept\n%s failed\n" % (passed, failed))
for criterion in criteria:
criterion.close()
def bam_cleancigar(infile, outfile):
bam = pysam.Samfile(infile, "rb")
out = pysam.Samfile(outfile, "wb", template=bam)
total = 0
count = 0
for read in bam_iter(bam):
if read_cleancigar(read):
count += 1
total += 1
out.write(read)
bam.close()
out.close()
sys.stderr.write('Wrote: %s reads\nAltered: %s\n' % (total, count))
def bam_cleancigar(infile, outfile):
bam = pysam.Samfile(infile, "rb")
out = pysam.Samfile(outfile, "wb", template=bam)
total = 0
count = 0
for read in bam_iter(bam):
if read_cleancigar(read):
count += 1
total += 1
out.write(read)
bam.close()
out.close()
sys.stderr.write('Wrote: %s reads\nAltered: %s\n' % (total, count))
def bam_split(infile,
out_template,
read_count=1000000,
reference=False,
quiet=False):
bamfile = pysam.Samfile(infile, "rb")
outfile = None
file_count = 0
count = 0
fname = ""
lastref = -1
for read in bam_iter(bamfile):
if not outfile or (not reference and count >= read_count) or (
reference and lastref != read.tid):
if outfile:
outfile.close()
file_count += 1
count = 0
if reference:
if read.tid >= 0:
fname = '%s.%s.bam' % (out_template,
bamfile.getrname(read.tid))
else:
fname = None
else:
fname = '%s.%s.bam' % (out_template, file_count)
if fname:
outfile = pysam.Samfile(fname, "wb", template=bamfile)
else:
outfile = None
if outfile:
outfile.write(read)
count += 1
lastref = read.tid
bamfile.close()
if outfile:
outfile.close()
if not quiet:
sys.stderr.write("Split into %s files" % (file_count))
def bam_tofastx(fname,
colorspace=False,
show_mapped=True,
show_unmapped=True,
fastq=True,
read1=True,
read2=True,
proper=False):
if show_mapped is False and show_unmapped is False:
return
sam = bam_open(fname)
last_key = None
for read in bam_iter(sam):
if not read1 and read.is_read1:
continue
if not read2 and read.is_read2:
continue
if proper and not read.is_proper_pair:
continue
k = (read.qname, read.seq)
if last_key == k:
continue
show = False
if show_mapped and not read.is_unmapped:
show = True
if show_unmapped and read.is_unmapped:
show = True
if not show:
continue
if fastq:
write_fastq(read, colorspace=colorspace)
else:
write_fasta(read, colorspace=colorspace)
last_key = k
def bam_junction_count(bam, ref=None, start=None, end=None, out=sys.stdout, quiet=False):
last_tid = None
junctions = {}
for read in bam_iter(bam, ref=ref, start=start, end=end, quiet=quiet):
if read.is_unmapped:
continue
if read.tid != last_tid and junctions:
for junction in junctions:
sys.stdout.write('%s\t%s\n' % (junction, len(junctions[junction])))
junctions = {}
last_tid = read.tid
hasgap = False
pos = read.pos
end = None
for op, size in read.cigar:
if op == 0:
pos += size
elif op == 1:
pass
elif op == 2:
pos += size
elif op == 3:
hasgap = True
end = pos + size
break
elif op == 4:
pos += size
if not hasgap:
continue
junction = '%s:%s-%s' % (bam.references[read.tid], pos, end)
if not junction in junctions:
junctions[junction] = set()
junctions[junction].add(read.qname)
for junction in junctions:
sys.stdout.write('%s\t%s\n' % (junction, len(junctions[junction])))
def bam_removeclipping(infile, outfile):
bam = pysam.Samfile(infile, "rb")
out = pysam.Samfile(outfile, "wb", template=bam)
total = 0
count = 0
unmapped = 0
for read in bam_iter(bam):
code = read_removeclipping(read)
if code == 1:
unmapped += 1
elif code == 2:
count += 1
total += 1
out.write(read)
bam.close()
out.close()
sys.stderr.write('Wrote: %s reads\nAltered: %s\nUnmapped: %s\n' % (total, count, unmapped))
def bam_export(bam,
mapped=True,
unmapped=True,
whitelist=None,
blacklist=None,
fields=None,
out=sys.stdout,
quiet=False):
for read in bam_iter(bam, quiet=quiet):
if whitelist and not read.qname in whitelist:
continue
if blacklist and read.qname in blacklist:
continue
try:
if mapped and not read.is_unmapped:
export_read(bam, read, fields, out)
elif unmapped and read.is_unmapped:
export_read(bam, read, fields, out)
except IOError:
break
def get_counts(self, bam, ref=None, start=None, end=None, quiet=False):
for read in bam_iter(bam, ref=ref, start=start, end=end, quiet=quiet, callback=lambda x: '%s:%s (%s)' % (self.cur_chrom, x.pos, len(self.pos_counts) if self.pos_counts else 0)):
if read.is_unmapped:
continue
if self.strand:
if self.strand == '+' and read.is_reverse:
continue
elif self.strand == '-' and not read.is_reverse:
continue
if self.cur_tid is None or read.tid != self.cur_tid:
if self.pos_counts:
self.flush()
self.pos_counts = array('I', [0,] * bam.lengths[read.tid])
self.cur_tid = read.tid
self.cur_chrom = bam.references[read.tid]
self._add_read(read)
self.flush()
def bam_split(infile, out_template, read_count=1000000, reference=False, quiet=False):
bamfile = pysam.Samfile(infile, "rb")
outfile = None
file_count = 0
count = 0
fname = ""
lastref = -1
for read in bam_iter(bamfile):
if not outfile or (not reference and count >= read_count) or (reference and lastref != read.tid):
if outfile:
outfile.close()
file_count += 1
count = 0
if reference:
if read.tid >= 0:
fname = '%s.%s.bam' % (out_template, bamfile.getrname(read.tid))
else:
fname = None
else:
fname = '%s.%s.bam' % (out_template, file_count)
if fname:
outfile = pysam.Samfile(fname, "wb", template=bamfile)
else:
outfile = None
if outfile:
outfile.write(read)
count += 1
lastref = read.tid
bamfile.close()
if outfile:
outfile.close()
if not quiet:
sys.stderr.write("Split into %s files" % (file_count))
def bam_tofastx(fname, colorspace=False, show_mapped=True, show_unmapped=True, fastq=True, read1=True, read2=True, proper=False):
if show_mapped is False and show_unmapped is False:
return
sam = bam_open(fname)
last_key = None
for read in bam_iter(sam):
if not read1 and read.is_read1:
continue
if not read2 and read.is_read2:
continue
if proper and not read.is_proper_pair:
continue
k = (read.qname, read.seq)
if last_key == k:
continue
show = False
if show_mapped and not read.is_unmapped:
show = True
if show_unmapped and read.is_unmapped:
show = True
if not show:
continue
if fastq:
write_fastq(read, colorspace=colorspace)
else:
write_fasta(read, colorspace=colorspace)
last_key = k
def pcrdup_mark(inbam, outbam, fragment=False, countfile=None):
cur_pos = None
cur_reads = {}
total = 0
unique = 0
duplicates = 0
dup_list = set()
def callback(read):
return '%s, %s, %s - %s' % (total, unique, duplicates, read.qname)
for read in bam_iter(bamfile, callback=callback):
if not read.is_paired or read.is_read1:
total += 1
if read.is_unmapped:
__flush_cur_reads(cur_reads, outbam, inbam, countfile)
if outbam:
outbam.write(read)
continue
start_pos = (read.tid, read.pos)
if fragment:
dup_pos = (read.tid, read.pos, '')
else:
# isize is the insert length, which if this is the first read, will
# be the right most part of the second read. If the ends of the reads
# are trimmed for QC reasons, only the 5' pos of the first read and the 3'
# pos of the second read will be accurate.
dup_pos = (read.tid, read.pos, read.isize)
if not cur_pos or start_pos != cur_pos:
__flush_cur_reads(cur_reads, outbam, inbam, countfile)
cur_pos = start_pos
cur_reads = {}
idx = 0
if not fragment and (read.mate_is_unmapped or not read.is_paired or not read.is_proper_pair or read.isize < 0):
# this is a paired file, but the mate isn't paired or proper or mapped
# just write it out, no flags to set.
if read.qname in dup_list:
read.is_duplicate = True
dup_list.remove(read.qname)
if outbam:
outbam.write(read)
elif dup_pos in cur_reads:
duplicates += 1
if not fragment:
dup_list.add(read.qname)
cur_reads[dup_pos].append((read.mapq, -idx, read))
else:
unique += 1
cur_reads[dup_pos] = [(read.mapq, -idx, read), ]
idx += 1
__flush_cur_reads(cur_reads, outbam, inbam, countfile)
sys.stdout.write('Total reads:\t%s\n' % total)
sys.stdout.write('Unique reads:\t%s\n' % unique)
sys.stdout.write('PCR duplicates:\t%s\n' % duplicates)
def _gen2():
def callback(read):
return '%s:%s (%s) %s:%s-%s' % (self.bam.getrname(read.tid), read.pos, len(self.buffer), self.cur_chrom, self.cur_start, self.cur_end)
for read in bam_iter(self.bam, quiet=self.quiet, callback=callback):
yield read
def bam_tobed(fname, out=sys.stdout):
bamfile = pysam.Samfile(fname, "rb")
for read in bam_iter(bamfile):
write_read(read, bamfile.getrname(read.rname), out)
bamfile.close()
def filter(self):
for read in bam_iter(self.bamfile):
yield read
self.bamfile.close()
def filter(self, bam):
for read in bam_iter(bam):
yield read
def _foo2():
for read in bam_iter(bamfile):
yield read
def _foo2():
for read in bam_iter(bamfile):
yield read
def _gen2():
def callback(read):
return '%s:%s (%s) %s:%s-%s' % (self.bam.getrname(read.tid), read.pos, len(self.buffer), self.cur_chrom, self.cur_start, self.cur_end)
for read in bam_iter(self.bam, quiet=self.quiet, callback=callback):
yield read
def filter(self, bam):
for read in bam_iter(bam):
yield read
def bam_innerdist(bam1, bam2, summaryout=None):
iter1 = bam_iter(bam1)
iter2 = bam_iter(bam2, quiet=True)
distances = {}
total = 0
proper = 0
orientation_count = {
'+/-': 0,
'-/+': 0,
'+/+': 0,
'-/-': 0,
}
read1_last = None
read2_last = None
read1 = None
read2 = None
while True:
try:
while not read1 or read1_last == read1.qname:
read1 = iter1.next()
while not read2 or read2_last == read2.qname:
read2 = iter2.next()
except StopIteration:
break
if read1.qname != read2.qname:
raise ValueError(
"Error: BAM files aren't properly paired! (%s, %s)\n" %
(read1.qname, read2.qname))
read1_last = read1.qname
read2_last = read2.qname
total += 1
if read1.is_unmapped or read2.is_unmapped or read1.tid != read2.tid:
continue
proper += 1
if read1.pos < read2.pos:
dist = read2.pos - read1.aend
else:
dist = read1.pos - read2.aend
if summaryout:
summaryout.write('%s\n' % dist)
if not dist in distances:
distances[dist] = 1
else:
distances[dist] += 1
orientation = '%s/%s' % ('-' if read1.is_reverse else '+',
'-' if read2.is_reverse else '+')
orientation_count[orientation] += 1
mean, stdev = counts_mean_stdev(distances)
return total, proper, mean, stdev, orientation_count
def bam_tobed(fname, out=sys.stdout):
bamfile = pysam.Samfile(fname, "rb")
for read in bam_iter(bamfile):
write_read(read, bamfile.getrname(read.rname), out)
bamfile.close()
