def _bowtie_for_innerdist(start, fastq_file, pair_file, ref_file, out_base,
out_dir, config, remove_workdir=False):
work_dir = os.path.join(out_dir, "innerdist_estimate")
if os.path.exists(work_dir):
shutil.rmtree(work_dir)
safe_makedir(work_dir)
extra_args = ["-s", str(start), "-u", "250000"]
out_sam = bowtie.align(fastq_file, pair_file, ref_file, out_base,
work_dir, config, extra_args)
dists = []
with closing(pysam.Samfile(out_sam)) as work_sam:
for read in work_sam:
if not read.is_unmapped and read.is_read1:
dists.append(abs(read.isize) - 2 * read.rlen)
return dists
def _bowtie_for_innerdist(start, fastq_file, pair_file, ref_file, out_base,
out_dir, config, remove_workdir=False):
work_dir = os.path.join(out_dir, "innerdist_estimate")
if os.path.exists(work_dir):
shutil.rmtree(work_dir)
safe_makedir(work_dir)
extra_args = ["-s", str(start), "-u", "250000"]
out_sam = bowtie.align(fastq_file, pair_file, ref_file, out_base,
work_dir, config, extra_args)
dists = []
with closing(pysam.Samfile(out_sam)) as work_sam:
for read in work_sam:
if not read.is_unmapped and read.is_read1:
dists.append(abs(read.isize) - 2 * read.rlen)
return dists
def _estimate_paired_innerdist(fastq_file, pair_file, ref_file, out_base,
out_dir, config):
"""Use Bowtie to estimate the inner distance of paired reads.
"""
work_dir = os.path.join(out_dir, "innerdist_estimate")
safe_makedir(work_dir)
extra_args = ["-s", "1000000", "-u", "250000"]
out_sam = bowtie.align(fastq_file, pair_file, ref_file, out_base,
work_dir, config, extra_args)
dists = []
with closing(pysam.Samfile(out_sam)) as work_sam:
for read in work_sam:
if not read.is_unmapped and read.is_read1:
dists.append(abs(read.isize) - 2 * read.rlen)
return int(round(numpy.mean(dists))), int(round(numpy.std(dists)))