def is_paired(bam_file):
"""Determine if a BAM file has paired reads.
Works around issues with head closing the samtools pipe using signal trick from:
http://stackoverflow.com/a/12451083/252589
"""
bam_file = objectstore.cl_input(bam_file)
cmd = ("set -o pipefail; "
"samtools view -h {bam_file} | head -300000 | "
"samtools view -S -f 1 /dev/stdin | head -1 | wc -l")
p = subprocess.Popen(
cmd.format(**locals()),
shell=True,
executable=do.find_bash(),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
preexec_fn=lambda: signal.signal(signal.SIGPIPE, signal.SIG_DFL))
stdout, stderr = p.communicate()
stdout = stdout.decode()
stderr = stderr.decode()
stderr = stderr.strip()
if ((p.returncode == 0 or p.returncode == 141) and
(stderr == "" or
(stderr.startswith("gof3r") and stderr.endswith("broken pipe")))):
return int(stdout) > 0
else:
raise ValueError("Failed to check paired status of BAM file: %s" %
str(stderr))
def _merge_and_bgzip(orig_files, out_file, base_file, ext=""):
"""Merge a group of gzipped input files into a final bgzipped output.
Also handles providing unique names for each input file to avoid
collisions on multi-region output. Handles renaming with awk magic from:
https://www.biostars.org/p/68477/
Removes orig_files after merging.
"""
assert out_file.endswith(".gz")
full_file = out_file.replace(".gz", "")
run_file = "%s-merge.bash" % utils.splitext_plus(base_file)[0]
cmds = ["set -e\n"]
for i, fname in enumerate(orig_files):
cmd = ("""zcat %s | awk '{print (NR%%4 == 1) ? "@%s_" ++i "%s" : $0}' >> %s\n"""
% (fname, i, ext, full_file))
cmds.append(cmd)
cmds.append("bgzip %s\n" % full_file)
with open(run_file, "w") as out_handle:
out_handle.write("".join("".join(cmds)))
do.run([do.find_bash(), run_file], "Rename, merge and bgzip CRAM fastq output")
assert os.path.exists(out_file) and not _is_gzip_empty(out_file)
for fname in orig_files:
os.remove(fname)
def is_paired(bam_file):
"""Determine if a BAM file has paired reads.
"""
bam_file = objectstore.cl_input(bam_file)
cmd = "sambamba view -h {bam_file} | head -50000 | " "sambamba view -S -F paired /dev/stdin | head -1 | wc -l"
out = subprocess.check_output(
cmd.format(**locals()), shell=True, executable=do.find_bash(), stderr=open("/dev/null", "w")
)
return int(out) > 0
def is_paired(bam_file):
"""Determine if a BAM file has paired reads.
"""
bam_file = objectstore.cl_input(bam_file)
cmd = ("sambamba view -h {bam_file} | head -50000 | "
"sambamba view -S -F paired /dev/stdin | head -1 | wc -l")
out = subprocess.check_output(cmd.format(**locals()), shell=True,
executable=do.find_bash(),
stderr=open("/dev/null", "w"))
return int(out) > 0
def is_empty(bam_file):
"""Determine if a BAM file is empty
"""
bam_file = objectstore.cl_input(bam_file)
cmd = ("set -o pipefail; "
"samtools view {bam_file} | head -1 | wc -l")
p = subprocess.Popen(cmd.format(**locals()), shell=True,
executable=do.find_bash(),
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
preexec_fn=lambda: signal.signal(signal.SIGPIPE, signal.SIG_DFL))
stdout, stderr = p.communicate()
stderr = stderr.strip()
if ((p.returncode == 0 or p.returncode == 141) and
(stderr == "" or (stderr.startswith("gof3r") and stderr.endswith("broken pipe")))):
return int(stdout) == 0
else:
raise ValueError("Failed to check empty status of BAM file: %s" % str(stderr))
def is_empty(bam_file):
"""Determine if a BAM file is empty
"""
bam_file = objectstore.cl_input(bam_file)
sambamba = config_utils.get_program("sambamba", {})
cmd = ("set -o pipefail; "
"{sambamba} view {bam_file} | head -1 | wc -l")
p = subprocess.Popen(cmd.format(**locals()), shell=True,
executable=do.find_bash(),
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
preexec_fn=lambda: signal.signal(signal.SIGPIPE, signal.SIG_DFL))
stdout, stderr = p.communicate()
stderr = stderr.strip()
if ((p.returncode == 0 or p.returncode == 141) and
(stderr == "" or (stderr.startswith("gof3r") and stderr.endswith("broken pipe")))):
return int(stdout) == 0
else:
raise ValueError("Failed to check empty status of BAM file: %s" % str(stderr))
def is_paired(bam_file):
"""Determine if a BAM file has paired reads.
Works around issues with head closing the samtools pipe using signal trick from:
http://stackoverflow.com/a/12451083/252589
"""
bam_file = objectstore.cl_input(bam_file)
cmd = ("set -o pipefail; "
"sambamba view -h {bam_file} | head -50000 | "
"sambamba view -S -F paired /dev/stdin | head -1 | wc -l")
p = subprocess.Popen(cmd.format(**locals()), shell=True,
executable=do.find_bash(),
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
preexec_fn=lambda: signal.signal(signal.SIGPIPE, signal.SIG_DFL))
stdout, stderr = p.communicate()
if p.returncode == 0 or p.returncode == 141 and stderr.strip() == "":
return int(stdout) > 0
else:
raise ValueError("Failed to check paired status of BAM file: %s" % str(stderr))
