def _casava_report_to_metrics(run_info_file, casava_report, dirs):
"""Convert the supplied CASAVA demultiplex report into bcbb-style
metric files, based on the configuration in the run_info_file.
Metric files are written to the workdir
"""
metric_files = []
metrics = defaultdict(dict)
for report in casava_report:
for lane, data in dmx._parse_demultiplex_stats_htm(report).items():
for sequence, metric in data.items():
# Assert that we are not overwriting a previously parsed metric
assert not (lane in metrics and sequence in metrics[lane]), \
"Conflicting demultiplex metrics found for lane {} and index {}. " \
"This means that there are multiple demultiplex results for the same sample. " \
"Please review and rectify before proceeding!".format(lane,sequence)
metrics[lane][sequence] = metric
with open(run_info_file) as fh:
info = yaml.load(fh)
fc_name, fc_date = fc.get_flowcell_info(dirs["flowcell"])
for item in info:
metrics_file = "{}_{}_{}.bc_metrics".format(item["lane"], fc_date, fc_name)
multiplex = item.get("multiplex", [])
for plex in multiplex:
plex["lane"] = item["lane"]
dmx._write_demultiplex_metrics(multiplex, metrics, os.path.join(dirs["work"], metrics_file))
metric_files.append(metrics_file)
return metric_files
def _casava_report_to_metrics(run_info_file, casava_report, dirs):
"""Convert the supplied CASAVA demultiplex report into bcbb-style
metric files, based on the configuration in the run_info_file.
Metric files are written to the workdir
"""
metric_files = []
metrics = dmx._parse_demultiplex_stats_htm(casava_report)
with open(run_info_file) as fh:
info = yaml.load(fh)
fc_name, fc_date = fc.get_flowcell_info(dirs["flowcell"])
for item in info:
metrics_file = "{}_{}_{}.bc_metrics".format(item["lane"], fc_date, fc_name)
multiplex = item.get("multiplex", [])
for plex in multiplex:
plex["lane"] = item["lane"]
dmx._write_demultiplex_metrics(multiplex, metrics, os.path.join(dirs["work"], metrics_file))
metric_files.append(metrics_file)
return metric_files
def _casava_report_to_metrics(run_info_file, casava_report, dirs):
"""Convert the supplied CASAVA demultiplex report into bcbb-style
metric files, based on the configuration in the run_info_file.
Metric files are written to the workdir
"""
metric_files = []
metrics = dmx._parse_demultiplex_stats_htm(casava_report)
with open(run_info_file) as fh:
info = yaml.load(fh)
fc_name, fc_date = fc.get_flowcell_info(dirs["flowcell"])
for item in info:
metrics_file = "{}_{}_{}.bc_metrics".format(
item["lane"], fc_date, fc_name)
multiplex = item.get("multiplex", [])
for plex in multiplex:
plex["lane"] = item["lane"]
dmx._write_demultiplex_metrics(
multiplex, metrics, os.path.join(dirs["work"], metrics_file))
metric_files.append(metrics_file)
return metric_files
