def _collect_casava_qc(self):
qc_objects = []
read_setup = None
demux_stats = None
fcdir = os.path.join(os.path.abspath(self._meta.root_path),
self.pargs.flowcell)
# Get the fc_name, fc_date from RunInfo
parser = FlowcellRunMetricsParser(fcdir)
runinfo_xml = parser.parseRunInfo()
runparams = parser.parseRunParameters()
fc_date = runinfo_xml.get('Date', None)
fc_name = runinfo_xml.get('Flowcell', None)
fc_pos = runparams.get('FCPosition', '')
runinfo_csv = os.path.join(
os.path.join(self._meta.root_path, self.pargs.flowcell),
"{}.csv".format(fc_name))
if not os.path.exists(runinfo_csv):
LOG.warn("No such file {}: trying fallback SampleSheet.csv".format(
runinfo_csv))
runinfo_csv = os.path.join(
os.path.join(self._meta.root_path, self.pargs.flowcell),
"SampleSheet.csv")
runinfo = parser.parse_samplesheet_csv(runinfo_csv=runinfo_csv)
if modified_within_days(fcdir, self.pargs.mtime):
# Most of the code expects to have the flowcell position pre-pended to the flowcell id
fc_kw = dict(fc_date=fc_date,
fc_name="{}{}".format(fc_pos, fc_name))
fcobj = FlowcellRunMetricsDocument(**fc_kw)
fcobj["RunInfo"] = runinfo_xml
fcobj["RunParameters"] = runparams
fcobj["DemultiplexConfig"] = parser.parseDemultiplexConfig(**fc_kw)
fcobj["illumina"] = parser.parse_illumina_metrics(fullRTA=False,
**fc_kw)
fcobj["bc_metrics"] = parser.parse_bc_metrics(**fc_kw)
fcobj[
"undemultiplexed_barcodes"] = parser.parse_undemultiplexed_barcode_metrics(
**fc_kw)
fcobj["illumina"].update({
"Demultiplex_Stats":
parser.parse_demultiplex_stats_htm(**fc_kw)
})
fcobj["samplesheet_csv"] = runinfo
read_setup = fcobj["RunInfo"].get('Reads', [])
fcobj["run_setup"] = self._run_setup(read_setup)
demux_stats = fcobj["illumina"]["Demultiplex_Stats"]
qc_objects.append(fcobj)
qc_objects = self._parse_samplesheet(runinfo,
qc_objects,
fc_date,
"{}{}".format(fc_pos, fc_name),
fcdir,
demultiplex_stats=demux_stats,
setup=read_setup)
return qc_objects
def _collect_casava_qc(self):
qc_objects = []
read_setup = None
demux_stats = None
fcdir = os.path.join(os.path.abspath(self._meta.root_path), self.pargs.flowcell)
# Get the fc_name, fc_date from RunInfo
parser = FlowcellRunMetricsParser(fcdir)
runinfo_xml = parser.parseRunInfo()
runparams = parser.parseRunParameters()
fc_date = runinfo_xml.get('Date',None)
fc_name = runinfo_xml.get('Flowcell',None)
fc_pos = runparams.get('FCPosition','')
runinfo_csv = os.path.join(os.path.join(self._meta.root_path, self.pargs.flowcell), "{}.csv".format(fc_name))
if not os.path.exists(runinfo_csv):
LOG.warn("No such file {}: trying fallback SampleSheet.csv".format(runinfo_csv))
runinfo_csv = os.path.join(os.path.join(self._meta.root_path, self.pargs.flowcell), "SampleSheet.csv")
runinfo = parser.parse_samplesheet_csv(runinfo_csv=runinfo_csv)
if modified_within_days(fcdir, self.pargs.mtime):
# Most of the code expects to have the flowcell position pre-pended to the flowcell id
fc_kw = dict(fc_date = fc_date, fc_name="{}{}".format(fc_pos,fc_name))
fcobj = FlowcellRunMetricsDocument(**fc_kw)
fcobj["RunInfo"] = runinfo_xml
fcobj["RunParameters"] = runparams
fcobj["DemultiplexConfig"] = parser.parseDemultiplexConfig(**fc_kw)
fcobj["illumina"] = parser.parse_illumina_metrics(fullRTA=False, **fc_kw)
fcobj["bc_metrics"] = parser.parse_bc_metrics(**fc_kw)
fcobj["undemultiplexed_barcodes"] = parser.parse_undemultiplexed_barcode_metrics(**fc_kw)
fcobj["illumina"].update({"Demultiplex_Stats" : parser.parse_demultiplex_stats_htm(**fc_kw)})
fcobj["samplesheet_csv"] = runinfo
read_setup = fcobj["RunInfo"].get('Reads',[])
fcobj["run_setup"] = self._run_setup(read_setup)
demux_stats = fcobj["illumina"]["Demultiplex_Stats"]
qc_objects.append(fcobj)
qc_objects = self._parse_samplesheet(runinfo, qc_objects, fc_date, "{}{}".format(fc_pos,fc_name), fcdir, demultiplex_stats=demux_stats, setup=read_setup)
return qc_objects
