def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
# generic args
csv_cols = ['sample'] + list(ReadUnit._fields)
parser.add_argument(
'-i',
"--csv",
required=True,
help="CSV input file describing your samples using the"
" following columns: {} (sample and fq1 are mandatory; leave unknown fields empty)"
.format(", ".join("{}:{}".format(i + 1, c)
for i, c in enumerate(csv_cols))))
parser.add_argument('-o',
"--yaml",
required=True,
help="Output config (yaml) file")
parser.add_argument('-d',
'--delimiter',
default="\t",
help="Use this delimiter for CSV (default is <tab>)")
parser.add_argument('-f',
'--force-overwrite',
action='store_true',
help="Force overwriting of existing file")
parser.add_argument('-v',
'--verbose',
action='count',
default=0,
help="Increase verbosity")
parser.add_argument('-q',
'--quiet',
action='count',
default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10 * args.quiet - 10 * args.verbose)
if len(args.delimiter) != 1:
logger.fatal("Delimiter needs to be exactly one character")
sys.exit(1)
if not os.path.exists(args.csv):
logger.fatal("Input file %s does not exist", args.csv)
sys.exit(1)
if os.path.exists(args.yaml) and not args.force_overwrite:
logger.fatal("Cowardly refusing to overwrite existing file %s",
args.yaml)
sys.exit(1)
samples = dict()
readunits = dict()
with open(args.csv) as csvfile:
csvreader = csv.reader(csvfile, delimiter=args.delimiter)
for row in csvreader:
if len(row) == 0:
continue
logger.debug(
"DEBUG row %s",
"\t".join("{}:{}".format(k, v) for k, v in zip(csv_cols, row)))
if len(row) != len(csv_cols):
logger.fatal("Only found %s fields (require %s) in row: %s",
len(row), len(csv_cols), '\t'.join(row))
sys.exit(1)
sample_name = row[0]
ru_fields = row[1:]
ru_fields = [x if len(x.strip()) else None for x in ru_fields]
#sys.stderr.write("ru_fields={}".format(ru_fields) + "\n")
ru = ReadUnit._make(ru_fields)
if not ru.rg_id:
ru = ru._replace(rg_id=create_rg_id_from_ru(ru))
ru_key = key_for_readunit(ru)
readunits[ru_key] = dict(ru._asdict())
if sample_name not in samples:
samples[sample_name] = []
samples[sample_name].append(ru_key)
with open(args.yaml, 'w') as fh:
yaml.dump(dict(samples=samples), fh, default_flow_style=False)
yaml.dump(dict(readunits=readunits), fh, default_flow_style=False)
def main():
"""main function
"""
parser = argparse.ArgumentParser(description=__doc__)
# generic args
csv_cols = ['sample'] + list(ReadUnit._fields)
parser.add_argument('-i', "--csv", required=True,
help="CSV input file describing your samples using the"
" following columns: {} (sample and fq1 are mandatory; leave unknown fields empty)".format(
", ".join("{}:{}".format(i+1, c) for i, c in enumerate(csv_cols))))
parser.add_argument('-o', "--yaml", required=True,
help="Output config (yaml) file")
parser.add_argument('-d', '--delimiter', default="\t",
help="Use this delimiter for CSV (default is <tab>)")
parser.add_argument('-f', '--force-overwrite', action='store_true',
help="Force overwriting of existing file")
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no logging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
if len(args.delimiter) != 1:
logger.fatal("Delimiter needs to be exactly one character")
sys.exit(1)
if not os.path.exists(args.csv):
logger.fatal("Input file %s does not exist", args.csv)
sys.exit(1)
if os.path.exists(args.yaml) and not args.force_overwrite:
logger.fatal("Cowardly refusing to overwrite existing file %s", args.yaml)
sys.exit(1)
samples = dict()
readunits = dict()
with open(args.csv) as csvfile:
csvreader = csv.reader(csvfile, delimiter=args.delimiter)
for row in csvreader:
if len(row) == 0:
continue
logger.debug("DEBUG row %s", "\t".join("{}:{}".format(k, v) for k, v in zip(csv_cols, row)))
if len(row) != len(csv_cols):
logger.fatal("Only found %s fields (require %s) in row: %s", len(row), len(csv_cols), '\t'.join(row))
sys.exit(1)
sample_name = row[0]
ru_fields = row[1:]
ru_fields = [x if len(x.strip()) else None for x in ru_fields]
#sys.stderr.write("ru_fields={}".format(ru_fields) + "\n")
ru = ReadUnit._make(ru_fields)
if not ru.rg_id:
ru = ru._replace(rg_id=create_rg_id_from_ru(ru))
ru_key = key_for_readunit(ru)
readunits[ru_key] = dict(ru._asdict())
if sample_name not in samples:
samples[sample_name] = []
samples[sample_name].append(ru_key)
with open(args.yaml, 'w') as fh:
yaml.dump(dict(samples=samples), fh, default_flow_style=False)
yaml.dump(dict(readunits=readunits), fh, default_flow_style=False)
def main():
"""main function"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("-b", "--bcl2fastq", required=True,
help="bcl2fastq directory")
parser.add_argument("-o", "--outpref",
help="Output prefix used for created yaml files per MUX (default: bcl2fastq dir)")
parser.add_argument('-f', "--overwrite", action='store_true',
help="Overwrite existing files")
parser.add_argument('-n', "--dry-run", action='store_true',
help="Dry run")
parser.add_argument('-v', '--verbose', action='count', default=0,
help="Increase verbosity")
parser.add_argument('-q', '--quiet', action='count', default=0,
help="Decrease verbosity")
args = parser.parse_args()
# Repeateable -v and -q for setting logging level.
# See https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
# and https://gist.github.com/andreas-wilm/b6031a84a33e652680d4
# script -vv -> DEBUG
# script -v -> INFO
# script -> WARNING
# script -q -> ERROR
# script -qq -> CRITICAL
# script -qqq -> no loggerging at all
logger.setLevel(logging.WARN + 10*args.quiet - 10*args.verbose)
if not os.path.exists(args.bcl2fastq):
logger.fatal("out_dir %s does not exist", args.bcl2fastq)
sys.exit(1)
confinfo = os.path.join(args.bcl2fastq + '/conf.yaml')
if not os.path.exists(confinfo):
logger.fatal("conf info '%s' does not exist under Run directory.\n", confinfo)
sys.exit(1)
if args.outpref:
outprefix = args.outpref
else:
outprefix = args.bcl2fastq
# FIXME too many levels of nesting. export to functions
with open(confinfo) as fh_cfg:
yaml_data = yaml.safe_load(fh_cfg)
assert "units" in yaml_data
assert "run_num" in yaml_data
run_num = yaml_data["run_num"]
for mux, units in yaml_data["units"].items():
mux_id = mux.split("_")[-1]
mux_folder = os.path.join(args.bcl2fastq, "out", mux)
if not os.path.exists(mux_folder):
continue
# samples and readunits per mux
samples = {}
readunits = {}
for child in os.listdir(os.path.join(args.bcl2fastq, "out", mux)):
if not child.startswith('Sample'):
continue
sample_id = child.split('_')[-1]
samples[sample_id] = []
sample_path = os.path.join(args.bcl2fastq, "out", mux, child)
for lane_id in units["lane_ids"]:
status, fq1, fq2 = check_fastq(sample_path, lane_id)
if not status:
# FIXME throw error?
continue
ru = ReadUnit(run_num, units["flowcell_id"], sample_id,
lane_id, None, fq1, fq2)
ru = ru._replace(rg_id=create_rg_id_from_ru(ru))
k = key_for_readunit(ru)
readunits[k] = dict(ru._asdict())
samples[sample_id].append(k)
# write yaml per mux
muxinfo_cfg = outprefix + mux_id + ".yaml"
if args.dry_run:
logger.warning("Skipped creation of %s", muxinfo_cfg)
else:
if os.path.exists(muxinfo_cfg) and not args.overwrite:
logger.fatal("Refusing to overwrite existing file %s", muxinfo_cfg)
sys.exit(1)
with open(muxinfo_cfg, 'w') as fh:
fh.write(yaml.dump(dict(samples=samples), default_flow_style=False))
fh.write(yaml.dump(dict(readunits=readunits), default_flow_style=False))
logger.info("Created %s", muxinfo_cfg)