def merge_sample_config(flist, sample):
"""Merge sample config files, making unique lanes if necessary.
Also write absolute paths to input sequence files. This will remove the multiplex key and place all configurations lane-wise.
:param flist: list of configuration files
:param sample: sample name to be used in description field for merging
:returns: merged configuration
"""
newconf = {'details':[]}
lane = 1
for f in flist:
with open(f) as fh:
conf = yaml.load(fh)
runinfo = conf.get("details") if conf.get("details", None) else conf
for i in range(0, len(runinfo)):
for j in range(0, len(runinfo[i].get("multiplex"))):
seqfiles = [os.path.join(os.path.dirname(f), x) for x in runinfo[i]["multiplex"][0]["files"]]
info = {}
info["lane"] = str(lane)
info["analysis"] = runinfo[i]["analysis"]
info["description"] = str(sample)
info["files"] = seqfiles
info["genome_build"] = runinfo[i]["genome_build"]
newconf['details'].append(info)
lane = lane + 1
(fc_name, fc_date) = _unique_flowcell_info()
newconf['fc_date'] = fc_date
newconf['fc_name'] = "TOTAL"
return newconf
def merge_sample_config(flist, sample, out_d, dry_run=True):
"""Merge sample config files, making unique lanes if necessary.
Also copies sequence files with rsync to the output directory.
This is a workaround for the case where sequence file names are
identical for different flowcell runs, causing the pipeline to
crash.
:param flist: list of configuration files
:param sample: sample name to be used in description field for merging
:param out_d: output directory
:returns: merged configuration
"""
newconf = {'details': []}
lane = 1
for f in flist:
with open(f) as fh:
conf = yaml.load(fh)
# Make sure the fastq files exist
conf = sort_sample_config_fastq(conf)
runinfo = conf.get("details") if conf.get("details", None) else conf
for i in range(0, len(runinfo)):
for j in range(0, len(runinfo[i].get("multiplex"))):
seqfiles = [
os.path.join(os.path.dirname(f), x)
for x in runinfo[i]["multiplex"][0]["files"]
]
target_seqfiles = [
os.path.join(
out_d,
os.path.basename(x).replace(
sample, "{}_{}".format(sample,
runinfo[i]["flowcell_id"])))
for x in seqfiles
]
[
dry_rsync(src, tgt, dry_run=dry_run)
for src, tgt in izip(seqfiles, target_seqfiles)
]
info = {}
info["lane"] = str(lane)
info["analysis"] = runinfo[i]["analysis"]
info["description"] = str(sample)
info["files"] = target_seqfiles
info["genome_build"] = runinfo[i]["genome_build"]
newconf['details'].append(info)
lane = lane + 1
(fc_name, fc_date) = _unique_flowcell_info()
newconf['fc_date'] = fc_date
newconf['fc_name'] = "TOTAL"
return newconf
def merge_sample_config(flist, sample, out_d, dry_run=True):
"""Merge sample config files, making unique lanes if necessary.
Also copies sequence files with rsync to the output directory.
This is a workaround for the case where sequence file names are
identical for different flowcell runs, causing the pipeline to
crash.
:param flist: list of configuration files
:param sample: sample name to be used in description field for merging
:param out_d: output directory
:returns: merged configuration
"""
newconf = {'details':[]}
lane = 1
for f in flist:
with open(f) as fh:
conf = yaml.load(fh)
# Make sure the fastq files exist
conf = sort_sample_config_fastq(conf)
runinfo = conf.get("details") if conf.get("details", None) else conf
for i in range(0, len(runinfo)):
for j in range(0, len(runinfo[i].get("multiplex"))):
seqfiles = [os.path.join(os.path.dirname(f), x) for x in runinfo[i]["multiplex"][0]["files"]]
target_seqfiles = [os.path.join(out_d, os.path.basename(x).replace(sample, "{}_{}".format(sample, runinfo[i]["flowcell_id"]))) for x in seqfiles]
[dry_rsync(src, tgt, dry_run=dry_run) for src, tgt in izip(seqfiles, target_seqfiles)]
info = {}
info["lane"] = str(lane)
info["analysis"] = runinfo[i]["analysis"]
info["description"] = str(sample)
info["files"] = target_seqfiles
info["genome_build"] = runinfo[i]["genome_build"]
newconf['details'].append(info)
lane = lane + 1
(fc_name, fc_date) = _unique_flowcell_info()
newconf['fc_date'] = fc_date
newconf['fc_name'] = "TOTAL"
return newconf
