def sam_to_bam_pesr(input_sam_file, input_fastq_file, output_bam_file):
samfh = pysam.Samfile(input_sam_file, "r")
fqiter = parse_fastq_record(open(input_fastq_file))
bamfh = pysam.Samfile(output_bam_file, "wb", template=samfh)
num_reads = 0
# get first fastq record
fqrec = fqiter.next()
for r in samfh:
# get next fastq record
if r.qname != fqrec.qname:
fqrec = fqiter.next()
# TODO: eventually remove assert statement
assert r.qname == fqrec.qname
# remove mate number from qname
r.qname = r.qname[1:]
# pad read that has been trimmed
soft_pad_read(fqrec, r)
# reset paired-end flags for read
r.is_paired = True
if fqrec.readnum == 1:
r.is_read1 = True
elif fqrec.readnum == 2:
r.is_read2 = True
else:
assert False
# TODO: remove is_secondary bit here because this does not
# make sense in the context of paired-end alignments
r.is_secondary = False
bamfh.write(r)
num_reads += 1
logging.debug("Found %d reads" % (num_reads))
bamfh.close()
samfh.close()
return config.JOB_SUCCESS
def sam_to_bam_pesr(input_sam_file, input_fastq_file, output_bam_file):
samfh = pysam.Samfile(input_sam_file, "r")
fqiter = parse_fastq_record(open(input_fastq_file))
bamfh = pysam.Samfile(output_bam_file, "wb", template=samfh)
num_reads = 0
# get first fastq record
fqrec = fqiter.next()
for r in samfh:
# get next fastq record
if r.qname != fqrec.qname:
fqrec = fqiter.next()
# TODO: eventually remove assert statement
assert r.qname == fqrec.qname
# remove mate number from qname
r.qname = r.qname[1:]
# pad read that has been trimmed
soft_pad_read(fqrec, r)
# reset paired-end flags for read
r.is_paired = True
if fqrec.readnum == 1:
r.is_read1 = True
elif fqrec.readnum == 2:
r.is_read2 = True
else:
assert False
# TODO: remove is_secondary bit here because this does not
# make sense in the context of paired-end alignments
r.is_secondary = False
bamfh.write(r)
num_reads += 1
logging.debug("Found %d reads" % (num_reads))
bamfh.close()
samfh.close()
return config.JOB_SUCCESS
def sam_to_bam(input_fastq_files,
input_sam_file,
output_bam_file,
quals,
multihits,
pe_sr_mode=False,
softclip=True,
keep_unmapped=True):
samfh = pysam.Samfile(input_sam_file, "r")
num_unmapped = 0
num_multihits = 0
num_frags = 0
bamfh = pysam.Samfile(output_bam_file, "wb", template=samfh)
# setup fastq parsing
if softclip and (quals != SANGER_FORMAT):
kwargs = {"convert_quals": True, "qual_format": quals}
else:
kwargs = {"convert_quals": False}
fqiters = [
parse_fastq_record(open(fq), **kwargs) for fq in input_fastq_files
]
# handle single-read and paired-end
if len(fqiters) == 1:
reorder_func = fix_sr_alignment_ordering(samfh, fqiters[0])
else:
reorder_func = fix_alignment_ordering(samfh, fqiters, pe_sr_mode)
# iterate through buffer
for bufitems in reorder_func:
num_frags += 1
for bufitem in bufitems:
for r in bufitem.reads:
# softclip uses the fastq record to replace the sequence
# and quality scores of the read
if softclip:
soft_pad_read(bufitem.fqrec, r)
# keep statistics of unmapped/multimapped reads and
# suppress output if 'keep_unmapped' is False
if r.is_unmapped:
xm_tag = r.opt('XM')
if xm_tag < multihits:
num_unmapped += 1
if not keep_unmapped:
continue
else:
num_multihits += 1
bamfh.write(r)
for fqfh in fqiters:
fqfh.close()
bamfh.close()
samfh.close()
logging.debug("Found %d fragments" % (num_frags))
logging.debug("\t%d unmapped reads" % (num_unmapped))
logging.debug("\t%d multimapping (>%dX) reads" %
(num_multihits, multihits))
def sam_to_bam(input_fastq_files, input_sam_file, output_bam_file,
quals, multihits, pe_sr_mode=False, softclip=True,
keep_unmapped=True):
samfh = pysam.Samfile(input_sam_file, "r")
num_unmapped = 0
num_multihits = 0
num_frags = 0
bamfh = pysam.Samfile(output_bam_file, "wb", template=samfh)
# setup fastq parsing
if softclip and (quals != SANGER_FORMAT):
kwargs = {"convert_quals": True, "qual_format": quals}
else:
kwargs = {"convert_quals": False}
fqiters = [parse_fastq_record(open(fq), **kwargs) for fq in input_fastq_files]
# handle single-read and paired-end
if len(fqiters) == 1:
reorder_func = fix_sr_alignment_ordering(samfh, fqiters[0])
else:
reorder_func = fix_alignment_ordering(samfh, fqiters, pe_sr_mode)
# iterate through buffer
for bufitems in reorder_func:
num_frags += 1
for bufitem in bufitems:
for r in bufitem.reads:
# softclip uses the fastq record to replace the sequence
# and quality scores of the read
if softclip:
soft_pad_read(bufitem.fqrec, r)
# keep statistics of unmapped/multimapped reads and
# suppress output if 'keep_unmapped' is False
if r.is_unmapped:
xm_tag = r.opt('XM')
if xm_tag < multihits:
num_unmapped += 1
if not keep_unmapped:
continue
else:
num_multihits += 1
bamfh.write(r)
for fqfh in fqiters:
fqfh.close()
bamfh.close()
samfh.close()
logging.debug("Found %d fragments" % (num_frags))
logging.debug("\t%d unmapped reads" % (num_unmapped))
logging.debug("\t%d multimapping (>%dX) reads" %
(num_multihits, multihits))
