def _run_snpeff(snp_in, out_format, data):
"""Run effects prediction with snpEff, skipping if snpEff database not present.
"""
snpeff_db, datadir = get_db(data)
if not snpeff_db:
return None, None
assert os.path.exists(os.path.join(datadir, snpeff_db)), \
"Did not find %s snpEff genome data in %s" % (snpeff_db, datadir)
ext = utils.splitext_plus(snp_in)[1] if out_format == "vcf" else ".tsv"
out_file = "%s-effects%s" % (utils.splitext_plus(snp_in)[0], ext)
stats_file = "%s-stats.html" % utils.splitext_plus(out_file)[0]
csv_file = "%s-stats.csv" % utils.splitext_plus(out_file)[0]
if not utils.file_exists(out_file):
config_args = " ".join(_snpeff_args_from_config(data))
if ext.endswith(".gz"):
bgzip_cmd = "| %s -c" % tools.get_bgzip_cmd(data["config"])
else:
bgzip_cmd = ""
with file_transaction(data, out_file) as tx_out_file:
snpeff_cmd = _get_snpeff_cmd("eff", datadir, data, tx_out_file)
cmd = (
"{snpeff_cmd} {config_args} -noLog -i vcf -o {out_format} "
"-csvStats {csv_file} -s {stats_file} {snpeff_db} {snp_in} {bgzip_cmd} > {tx_out_file}"
)
do.run(cmd.format(**locals()), "snpEff effects", data)
if ext.endswith(".gz"):
out_file = vcfutils.bgzip_and_index(out_file, data["config"])
return out_file, [stats_file, csv_file]
def _run_snpeff(snp_in, out_format, data):
snpeff_db, datadir = get_db(data)
assert datadir is not None, "Did not find snpEff resources in genome configuration: %s" % data["genome_resources"]
assert os.path.exists(os.path.join(datadir, snpeff_db)), "Did not find %s snpEff genome data in %s" % (
snpeff_db,
datadir,
)
snpeff_cmd = get_cmd("eff", datadir, data["config"])
ext = utils.splitext_plus(snp_in)[1] if out_format == "vcf" else ".tsv"
out_file = "%s-effects%s" % (utils.splitext_plus(snp_in)[0], ext)
if not utils.file_exists(out_file):
config_args = " ".join(_snpeff_args_from_config(data))
if ext.endswith(".gz"):
bgzip_cmd = "| %s -c" % tools.get_bgzip_cmd(data["config"])
else:
bgzip_cmd = ""
with file_transaction(out_file) as tx_out_file:
cmd = (
"{snpeff_cmd} {config_args} -noLog -1 -i vcf -o {out_format} "
"{snpeff_db} {snp_in} {bgzip_cmd} > {tx_out_file}"
)
do.run(cmd.format(**locals()), "snpEff effects", data)
if ext.endswith(".gz"):
out_file = vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
def bgzip_and_index(in_file, config=None, remove_orig=True, prep_cmd="", tabix_args=None, out_dir=None):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
if config is None:
config = {}
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if out_dir:
remove_orig = False
out_file = os.path.join(out_dir, os.path.basename(out_file))
if (not utils.file_exists(out_file) or not os.path.lexists(out_file)
or (utils.file_exists(in_file) and not utils.file_uptodate(out_file, in_file))):
assert not in_file == out_file, "Input file is bgzipped but not found: %s" % in_file
assert os.path.exists(in_file), "Input file %s not found" % in_file
if not utils.file_uptodate(out_file, in_file):
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
if prep_cmd:
prep_cmd = "| %s " % prep_cmd
cmd = "{cat_cmd} {in_file} {prep_cmd} | {bgzip} -c > {tx_out_file}"
try:
do.run(cmd.format(**locals()), "bgzip %s" % os.path.basename(in_file))
except subprocess.CalledProcessError:
# Race conditions: ignore errors where file has been deleted by another
if os.path.exists(in_file) and not os.path.exists(out_file):
raise
if remove_orig:
try:
os.remove(in_file)
except OSError: # Handle cases where run in parallel and file has been deleted
pass
tabix_index(out_file, config, tabix_args=tabix_args)
return out_file
def bgzip_and_index(in_file, config, remove_orig=True, prep_cmd=""):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if not utils.file_exists(out_file) or not os.path.lexists(out_file):
assert not in_file == out_file, "Input file is bgzipped but not found: %s" % in_file
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
if prep_cmd:
cmd = "cat {in_file} | {prep_cmd} | {bgzip} -c > {tx_out_file}"
else:
cmd = "{bgzip} -c {in_file} > {tx_out_file}"
try:
do.run(cmd.format(**locals()),
"bgzip %s" % os.path.basename(in_file))
except subprocess.CalledProcessError:
# Race conditions: ignore errors where file has been deleted by another
if os.path.exists(in_file) and not os.path.exists(out_file):
raise
if remove_orig:
try:
os.remove(in_file)
except OSError: # Handle cases where run in parallel and file has been deleted
pass
tabix_index(out_file, config)
return out_file
def _run_snpeff(snp_in, out_format, data):
"""Run effects prediction with snpEff, skipping if snpEff database not present.
"""
snpeff_db, datadir = get_db(data)
if not snpeff_db:
return None
assert os.path.exists(os.path.join(datadir, snpeff_db)), \
"Did not find %s snpEff genome data in %s" % (snpeff_db, datadir)
snpeff_cmd = get_cmd("eff", datadir, data["config"])
ext = utils.splitext_plus(snp_in)[1] if out_format == "vcf" else ".tsv"
out_file = "%s-effects%s" % (utils.splitext_plus(snp_in)[0], ext)
if not utils.file_exists(out_file):
config_args = " ".join(_snpeff_args_from_config(data))
if ext.endswith(".gz"):
bgzip_cmd = "| %s -c" % tools.get_bgzip_cmd(data["config"])
else:
bgzip_cmd = ""
with file_transaction(data, out_file) as tx_out_file:
cmd = ("{snpeff_cmd} {config_args} -noLog -i vcf -o {out_format} "
"{snpeff_db} {snp_in} {bgzip_cmd} > {tx_out_file}")
do.run(cmd.format(**locals()), "snpEff effects", data)
if ext.endswith(".gz"):
out_file = vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
def _bgzip_file(in_file, dirs, config, needs_bgzip, needs_gunzip,
needs_convert):
"""Handle bgzip of input file, potentially gunzipping an existing file.
"""
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep"))
out_file = os.path.join(
work_dir,
os.path.basename(in_file) +
(".gz" if not in_file.endswith(".gz") else ""))
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
assert needs_bgzip
bgzip = tools.get_bgzip_cmd(config)
if needs_convert:
in_file = fastq_convert_pipe_cl(in_file, {"config": config})
if needs_gunzip:
gunzip_cmd = "gunzip -c {in_file} |".format(**locals())
bgzip_in = "/dev/stdin"
else:
gunzip_cmd = ""
bgzip_in = in_file
do.run(
"{gunzip_cmd} {bgzip} -c {bgzip_in} > {tx_out_file}".format(
**locals()), "bgzip input file")
return out_file
def _bgzip_file(in_file, dirs, config, needs_bgzip, needs_gunzip, needs_convert):
"""Handle bgzip of input file, potentially gunzipping an existing file.
"""
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep"))
out_file = os.path.join(work_dir, os.path.basename(in_file) +
(".gz" if not in_file.endswith(".gz") else ""))
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
is_remote = in_file.startswith(utils.SUPPORTED_REMOTES)
in_file = utils.remote_cl_input(in_file, unpack=needs_gunzip or needs_convert or needs_bgzip)
if needs_convert:
in_file = fastq_convert_pipe_cl(in_file, {"config": config})
if needs_gunzip:
gunzip_cmd = "gunzip -c {in_file} |".format(**locals())
bgzip_in = "/dev/stdin"
else:
gunzip_cmd = ""
bgzip_in = in_file
if needs_bgzip:
do.run("{gunzip_cmd} {bgzip} -c {bgzip_in} > {tx_out_file}".format(**locals()),
"bgzip input file")
elif is_remote:
do.run("cat {in_file} > {tx_out_file}".format(**locals()), "Get remote input")
else:
raise ValueError("Unexpected inputs: %s %s %s %s" % (in_file, needs_bgzip,
needs_gunzip, needs_convert))
return out_file
def _bgzip_file(in_file, config, work_dir, needs_bgzip, needs_gunzip, needs_convert):
"""Handle bgzip of input file, potentially gunzipping an existing file.
"""
out_file = os.path.join(work_dir, os.path.basename(in_file) +
(".gz" if not in_file.endswith(".gz") else ""))
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
is_remote = objectstore.is_remote(in_file)
in_file = objectstore.cl_input(in_file, unpack=needs_gunzip or needs_convert or needs_bgzip)
if needs_convert:
in_file = fastq_convert_pipe_cl(in_file, {"config": config})
if needs_gunzip and not needs_convert:
gunzip_cmd = "gunzip -c {in_file} |".format(**locals())
bgzip_in = "/dev/stdin"
else:
gunzip_cmd = ""
bgzip_in = in_file
if needs_bgzip:
do.run("{gunzip_cmd} {bgzip} -c {bgzip_in} > {tx_out_file}".format(**locals()),
"bgzip input file")
elif is_remote:
bgzip = "| bgzip -c" if needs_convert else ""
do.run("cat {in_file} {bgzip} > {tx_out_file}".format(**locals()), "Get remote input")
else:
raise ValueError("Unexpected inputs: %s %s %s %s" % (in_file, needs_bgzip,
needs_gunzip, needs_convert))
return out_file
def bgzip_and_index(in_file, config=None, remove_orig=True, prep_cmd="", tabix_args=None, out_dir=None):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
if config is None:
config = {}
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if out_dir:
remove_orig = False
out_file = os.path.join(out_dir, os.path.basename(out_file))
if (not utils.file_exists(out_file) or not os.path.lexists(out_file)
or (utils.file_exists(in_file) and not utils.file_uptodate(out_file, in_file))):
assert not in_file == out_file, "Input file is bgzipped but not found: %s" % in_file
assert os.path.exists(in_file), "Input file %s not found" % in_file
if not utils.file_uptodate(out_file, in_file):
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
if prep_cmd:
prep_cmd = "| %s " % prep_cmd
cmd = "{cat_cmd} {in_file} {prep_cmd} | {bgzip} -c > {tx_out_file}"
try:
do.run(cmd.format(**locals()), "bgzip %s" % os.path.basename(in_file))
except subprocess.CalledProcessError:
# Race conditions: ignore errors where file has been deleted by another
if os.path.exists(in_file) and not os.path.exists(out_file):
raise
if remove_orig:
try:
os.remove(in_file)
except OSError: # Handle cases where run in parallel and file has been deleted
pass
tabix_index(out_file, config, tabix_args=tabix_args)
return out_file
def bgzip_and_index(in_file, config, remove_orig=True, prep_cmd=""):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if not utils.file_exists(out_file) or not os.path.lexists(out_file):
assert not in_file == out_file, "Input file is bgzipped but not found: %s" % in_file
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
if prep_cmd:
cmd = "cat {in_file} | {prep_cmd} | {bgzip} -c > {tx_out_file}"
else:
cmd = "{bgzip} -c {in_file} > {tx_out_file}"
try:
do.run(cmd.format(**locals()), "bgzip %s" % os.path.basename(in_file))
except subprocess.CalledProcessError:
# Race conditions: ignore errors where file has been deleted by another
if os.path.exists(in_file) and not os.path.exists(out_file):
raise
if remove_orig:
try:
os.remove(in_file)
except OSError: # Handle cases where run in parallel and file has been deleted
pass
tabix_index(out_file, config)
return out_file
def _bgzip_from_bam(bam_file, dirs, config, is_retry=False, output_infix=''):
"""Create bgzipped fastq files from an input BAM file.
"""
# tools
bamtofastq = config_utils.get_program("bamtofastq", config)
resources = config_utils.get_resources("bamtofastq", config)
cores = config["algorithm"].get("num_cores", 1)
max_mem = config_utils.convert_to_bytes(resources.get("memory",
"1G")) * cores
bgzip = tools.get_bgzip_cmd(config, is_retry)
# files
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep"))
out_file_1 = os.path.join(
work_dir, "%s%s-1.fq.gz" %
(os.path.splitext(os.path.basename(bam_file))[0], output_infix))
out_file_2 = out_file_1.replace("-1.fq.gz", "-2.fq.gz")
needs_retry = False
if is_retry or not utils.file_exists(out_file_1):
if not bam.is_paired(bam_file):
out_file_2 = None
with file_transaction(config, out_file_1) as tx_out_file:
for f in [tx_out_file, out_file_1, out_file_2]:
if f and os.path.exists(f):
os.remove(f)
fq1_bgzip_cmd = "%s -c /dev/stdin > %s" % (bgzip, tx_out_file)
sortprefix = "%s-sort" % os.path.splitext(tx_out_file)[0]
if bam.is_paired(bam_file):
fq2_bgzip_cmd = "%s -c /dev/stdin > %s" % (bgzip, out_file_2)
out_str = (
"F=>({fq1_bgzip_cmd}) F2=>({fq2_bgzip_cmd}) S=/dev/null O=/dev/null "
"O2=/dev/null collate=1 colsbs={max_mem}")
else:
out_str = "S=>({fq1_bgzip_cmd})"
bam_file = objectstore.cl_input(bam_file)
cmd = "{bamtofastq} filename={bam_file} T={sortprefix} " + out_str
try:
do.run(cmd.format(**locals()),
"BAM to bgzipped fastq",
checks=[do.file_reasonable_size(tx_out_file, bam_file)],
log_error=False)
except subprocess.CalledProcessError as msg:
if not is_retry and "deflate failed" in str(msg):
logger.info(
"bamtofastq deflate IO failure preparing %s. Retrying with single core."
% (bam_file))
needs_retry = True
else:
logger.exception()
raise
if needs_retry:
return _bgzip_from_bam(bam_file, dirs, config, is_retry=True)
else:
return [
x for x in [out_file_1, out_file_2]
if x is not None and utils.file_exists(x)
]
def _bgzip_from_bam(bam_file, dirs, data, is_retry=False, output_infix=''):
"""Create bgzipped fastq files from an input BAM file.
"""
# tools
config = data["config"]
bamtofastq = config_utils.get_program("bamtofastq", config)
resources = config_utils.get_resources("bamtofastq", config)
cores = config["algorithm"].get("num_cores", 1)
max_mem = config_utils.convert_to_bytes(resources.get("memory", "1G")) * cores
bgzip = tools.get_bgzip_cmd(config, is_retry)
# files
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep"))
out_file_1 = os.path.join(work_dir, "%s%s-1.fq.gz" % (os.path.splitext(os.path.basename(bam_file))[0], output_infix))
out_file_2 = out_file_1.replace("-1.fq.gz", "-2.fq.gz")
needs_retry = False
if is_retry or not utils.file_exists(out_file_1):
if not bam.is_paired(bam_file):
out_file_2 = None
with file_transaction(config, out_file_1) as tx_out_file:
for f in [tx_out_file, out_file_1, out_file_2]:
if f and os.path.exists(f):
os.remove(f)
fq1_bgzip_cmd = "%s -c /dev/stdin > %s" % (bgzip, tx_out_file)
prep_cmd = _seqtk_fastq_prep_cl(data, read_num=0)
if prep_cmd:
fq1_bgzip_cmd = prep_cmd + " | " + fq1_bgzip_cmd
sortprefix = "%s-sort" % os.path.splitext(tx_out_file)[0]
if bam.is_paired(bam_file):
prep_cmd = _seqtk_fastq_prep_cl(data, read_num=1)
fq2_bgzip_cmd = "%s -c /dev/stdin > %s" % (bgzip, out_file_2)
if prep_cmd:
fq2_bgzip_cmd = prep_cmd + " | " + fq2_bgzip_cmd
out_str = ("F=>({fq1_bgzip_cmd}) F2=>({fq2_bgzip_cmd}) S=/dev/null O=/dev/null "
"O2=/dev/null collate=1 colsbs={max_mem}")
else:
out_str = "S=>({fq1_bgzip_cmd})"
bam_file = objectstore.cl_input(bam_file)
extra_opts = " ".join([str(x) for x in resources.get("options", [])])
cmd = "{bamtofastq} filename={bam_file} T={sortprefix} {extra_opts} " + out_str
try:
do.run(cmd.format(**locals()), "BAM to bgzipped fastq",
checks=[do.file_reasonable_size(tx_out_file, bam_file)],
log_error=False)
except subprocess.CalledProcessError as msg:
if not is_retry and "deflate failed" in str(msg):
logger.info("bamtofastq deflate IO failure preparing %s. Retrying with single core."
% (bam_file))
needs_retry = True
else:
logger.exception()
raise
if needs_retry:
return _bgzip_from_bam(bam_file, dirs, data, is_retry=True)
else:
return [x for x in [out_file_1, out_file_2] if x is not None and utils.file_exists(x)]
def bgzip_and_index(in_file, config):
"""bgzip and tabix index an input VCF file.
"""
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
cmd = "{bgzip} -c {in_file} > {tx_out_file}"
do.run(cmd.format(**locals()), "bgzip %s" % os.path.basename(in_file))
os.remove(in_file)
tabix_index(out_file, config)
return out_file
def _bgzip_file(finput, config, work_dir, needs_bgzip, needs_gunzip,
needs_convert, data):
"""Handle bgzip of input file, potentially gunzipping an existing file.
Handles cases where finput might be multiple files and need to be concatenated.
"""
if isinstance(finput, six.string_types):
in_file = finput
else:
assert not needs_convert, "Do not yet handle quality conversion with multiple inputs"
return _bgzip_multiple_files(finput, work_dir, data)
out_file = os.path.join(
work_dir,
os.path.basename(in_file).replace(".bz2", "") +
(".gz" if not in_file.endswith(".gz") else ""))
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
is_remote = objectstore.is_remote(in_file)
in_file = objectstore.cl_input(in_file,
unpack=needs_gunzip or needs_convert
or needs_bgzip
or dd.get_trim_ends(data))
if needs_convert or dd.get_trim_ends(data):
in_file = fastq_convert_pipe_cl(in_file, data)
if needs_gunzip and not (needs_convert or dd.get_trim_ends(data)):
if in_file.endswith(".bz2"):
gunzip_cmd = "bunzip2 -c {in_file} |".format(**locals())
else:
gunzip_cmd = "gunzip -c {in_file} |".format(**locals())
bgzip_in = "/dev/stdin"
else:
gunzip_cmd = ""
bgzip_in = in_file
if needs_bgzip:
do.run(
"{gunzip_cmd} {bgzip} -c {bgzip_in} > {tx_out_file}".
format(**locals()), "bgzip input file")
elif is_remote:
bgzip = "| bgzip -c" if (needs_convert
or dd.get_trim_ends(data)) else ""
do.run(
"cat {in_file} {bgzip} > {tx_out_file}".format(**locals()),
"Get remote input")
else:
raise ValueError(
"Unexpected inputs: %s %s %s %s" %
(in_file, needs_bgzip, needs_gunzip, needs_convert))
return out_file
def _bgzip_from_bam(bam_file, dirs, config, is_retry=False):
"""Create bgzipped fastq files from an input BAM file.
"""
# tools
bamtofastq = config_utils.get_program("bamtofastq", config)
resources = config_utils.get_resources("bamtofastq", config)
cores = config["algorithm"].get("num_cores", 1)
max_mem = int(resources.get("memory", "1073741824")) * cores # 1Gb/core default
bgzip = tools.get_bgzip_cmd(config, is_retry)
# files
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep"))
out_file_1 = os.path.join(work_dir, "%s-1.fq.gz" % os.path.splitext(os.path.basename(bam_file))[0])
if bam.is_paired(bam_file):
out_file_2 = out_file_1.replace("-1.fq.gz", "-2.fq.gz")
else:
out_file_2 = None
needs_retry = False
if is_retry or not utils.file_exists(out_file_1):
with file_transaction(config, out_file_1) as tx_out_file:
for f in [tx_out_file, out_file_1, out_file_2]:
if f and os.path.exists(f):
os.remove(f)
fq1_bgzip_cmd = "%s -c /dev/stdin > %s" % (bgzip, tx_out_file)
sortprefix = "%s-sort" % os.path.splitext(tx_out_file)[0]
if bam.is_paired(bam_file):
fq2_bgzip_cmd = "%s -c /dev/stdin > %s" % (bgzip, out_file_2)
out_str = ("F=>({fq1_bgzip_cmd}) F2=>({fq2_bgzip_cmd}) S=/dev/null O=/dev/null "
"O2=/dev/null collate=1 colsbs={max_mem}")
else:
out_str = "S=>({fq1_bgzip_cmd})"
bam_file = objectstore.cl_input(bam_file)
cmd = "{bamtofastq} filename={bam_file} T={sortprefix} " + out_str
try:
do.run(cmd.format(**locals()), "BAM to bgzipped fastq",
checks=[do.file_reasonable_size(tx_out_file, bam_file)],
log_error=False)
except subprocess.CalledProcessError, msg:
if not is_retry and "deflate failed" in str(msg):
logger.info("bamtofastq deflate IO failure preparing %s. Retrying with single core."
% (bam_file))
needs_retry = True
else:
logger.exception()
raise
def bgzip_and_index(in_file, config):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
cmd = "{bgzip} -c {in_file} > {tx_out_file}"
try:
do.run(cmd.format(**locals()), "bgzip %s" % os.path.basename(in_file))
except subprocess.CalledProcessError:
# Race conditions: ignore errors where file has been deleted by another
if os.path.exists(in_file) and not os.path.exists(out_file):
raise
try:
os.remove(in_file)
except OSError: # Handle cases where run in parallel and file has been deleted
pass
tabix_index(out_file, config)
return out_file
def _bgzip_file(in_file, dirs, config, needs_bgzip, needs_gunzip, needs_convert):
"""Handle bgzip of input file, potentially gunzipping an existing file.
"""
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep"))
out_file = os.path.join(work_dir, os.path.basename(in_file) +
(".gz" if not in_file.endswith(".gz") else ""))
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
assert needs_bgzip
bgzip = tools.get_bgzip_cmd(config)
if needs_convert:
in_file = fastq_convert_pipe_cl(in_file, {"config": config})
if needs_gunzip:
gunzip_cmd = "gunzip -c {in_file} |".format(**locals())
bgzip_in = "/dev/stdin"
else:
gunzip_cmd = ""
bgzip_in = in_file
do.run("{gunzip_cmd} {bgzip} -c {bgzip_in} > {tx_out_file}".format(**locals()),
"bgzip input file")
return out_file
def bgzip_and_index(in_file, config):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
cmd = "{bgzip} -c {in_file} > {tx_out_file}"
try:
do.run(cmd.format(**locals()),
"bgzip %s" % os.path.basename(in_file))
except subprocess.CalledProcessError:
# Race conditions: ignore errors where file has been deleted by another
if os.path.exists(in_file) and not os.path.exists(out_file):
raise
try:
os.remove(in_file)
except OSError: # Handle cases where run in parallel and file has been deleted
pass
tabix_index(out_file, config)
return out_file
def _bgzip_file(finput, config, work_dir, needs_bgzip, needs_gunzip, needs_convert, data):
"""Handle bgzip of input file, potentially gunzipping an existing file.
Handles cases where finput might be multiple files and need to be concatenated.
"""
if isinstance(finput, six.string_types):
in_file = finput
else:
assert not needs_convert, "Do not yet handle quality conversion with multiple inputs"
return _bgzip_multiple_files(finput, work_dir, data)
out_file = os.path.join(work_dir, os.path.basename(in_file).replace(".bz2", "") +
(".gz" if not in_file.endswith(".gz") else ""))
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bgzip = tools.get_bgzip_cmd(config)
is_remote = objectstore.is_remote(in_file)
in_file = objectstore.cl_input(in_file, unpack=needs_gunzip or needs_convert or
needs_bgzip or dd.get_trim_ends(data))
if needs_convert or dd.get_trim_ends(data):
in_file = fastq_convert_pipe_cl(in_file, data)
if needs_gunzip and not (needs_convert or dd.get_trim_ends(data)):
if in_file.endswith(".bz2"):
gunzip_cmd = "bunzip2 -c {in_file} |".format(**locals())
else:
gunzip_cmd = "gunzip -c {in_file} |".format(**locals())
bgzip_in = "/dev/stdin"
else:
gunzip_cmd = ""
bgzip_in = in_file
if needs_bgzip:
do.run("{gunzip_cmd} {bgzip} -c {bgzip_in} > {tx_out_file}".format(**locals()),
"bgzip input file")
elif is_remote:
bgzip = "| bgzip -c" if (needs_convert or dd.get_trim_ends(data)) else ""
do.run("cat {in_file} {bgzip} > {tx_out_file}".format(**locals()), "Get remote input")
else:
raise ValueError("Unexpected inputs: %s %s %s %s" % (in_file, needs_bgzip,
needs_gunzip, needs_convert))
return out_file
def _run_snpeff(snp_in, out_format, data):
snpeff_db, datadir = get_db(data)
assert datadir is not None, \
"Did not find snpEff resources in genome configuration: %s" % data["genome_resources"]
assert os.path.exists(os.path.join(datadir, snpeff_db)), \
"Did not find %s snpEff genome data in %s" % (snpeff_db, datadir)
snpeff_cmd = get_cmd("eff", datadir, data["config"])
ext = utils.splitext_plus(snp_in)[1] if out_format == "vcf" else ".tsv"
out_file = "%s-effects%s" % (utils.splitext_plus(snp_in)[0], ext)
if not utils.file_exists(out_file):
config_args = " ".join(_snpeff_args_from_config(data))
if ext.endswith(".gz"):
bgzip_cmd = "| %s -c" % tools.get_bgzip_cmd(data["config"])
else:
bgzip_cmd = ""
with file_transaction(out_file) as tx_out_file:
cmd = ("{snpeff_cmd} {config_args} -noLog -1 -i vcf -o {out_format} "
"{snpeff_db} {snp_in} {bgzip_cmd} > {tx_out_file}")
do.run(cmd.format(**locals()), "snpEff effects", data)
if ext.endswith(".gz"):
out_file = vcfutils.bgzip_and_index(out_file, data["config"])
return out_file