def test_get_bc_count_demux_stats(self):
parser = SampleRunMetricsParser(os.path.join(project_dir, "J.Doe_00_01", "P001_101_index3", "120924_AC003CCCXX"))
bc_count = parser.get_bc_count(**self.sample_kw)
fc_parser = FlowcellRunMetricsParser(self.fcdir)
data = fc_parser.parse_demultiplex_stats_htm(**self.fc_kw)
bc_count = parser.get_bc_count(demultiplex_stats=data, **self.sample_kw)
self.assertEqual(str(bc_count), str(19517198))
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 test_parseRunParameters(self):
parser = FlowcellRunMetricsParser(self.fcdir)
data = parser.parseRunParameters(**self.fc_kw)
self.assertEqual(
data['Setup']['FPGADynamicFocusSettings']['CVGainPosLocked'],
'500')
self.assertEqual(data['Setup']['Reads']['Read'][0]['NumCycles'], '101')
self.assertEqual(
data['Setup']['SelectedSections']['Section'][1]['Name'], 'B_1')
def __init__(self, run_dir, samplesheet=None):
self._run_dir = os.path.normpath(run_dir)
assert os.path.exists(self._run_dir), "The path %s is invalid" % self._run_dir
# Parse the run parameters
parser = FlowcellRunMetricsParser(self._run_dir)
self.run_config = parser.parseRunParameters()
self.run_info = parser.parseRunInfo()
self.samplesheet_file = samplesheet or IlluminaRun.get_samplesheet(self._run_dir)
def test_get_bc_count_demux_stats(self):
parser = SampleRunMetricsParser(
os.path.join(project_dir, "J.Doe_00_01", "P001_101_index3",
"120924_AC003CCCXX"))
bc_count = parser.get_bc_count(**self.sample_kw)
fc_parser = FlowcellRunMetricsParser(self.fcdir)
data = fc_parser.parse_demultiplex_stats_htm(**self.fc_kw)
bc_count = parser.get_bc_count(demultiplex_stats=data,
**self.sample_kw)
self.assertEqual(str(bc_count), str(19517198))
def _collect_casava_qc(self):
qc_objects = []
runinfo_csv = os.path.join(os.path.join(self._meta.root_path, self.pargs.flowcell), "{}.csv".format(fc_id(self.pargs.flowcell)))
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")
try:
with open(runinfo_csv) as fh:
runinfo_reader = csv.reader(fh)
runinfo = [x for x in runinfo_reader]
except IOError as e:
self.app.log.warn(str(e))
raise e
fcdir = os.path.join(os.path.abspath(self._meta.root_path), self.pargs.flowcell)
(fc_date, fc_name) = fc_parts(self.pargs.flowcell)
## Check modification time
demux_stats = None
if modified_within_days(fcdir, self.pargs.mtime):
fc_kw = dict(fc_date = fc_date, fc_name=fc_name)
parser = FlowcellRunMetricsParser(fcdir)
fcobj = FlowcellRunMetricsDocument(fc_date, fc_name)
fcobj["RunInfo"] = parser.parseRunInfo(**fc_kw)
fcobj["RunParameters"] = parser.parseRunParameters(**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"] = parser.parse_samplesheet_csv(runinfo_csv=runinfo_csv, **fc_kw)
demux_stats = fcobj["illumina"]["Demultiplex_Stats"]
qc_objects.append(fcobj)
qc_objects = self._parse_samplesheet(runinfo, qc_objects, fc_date, fc_name, fcdir, demultiplex_stats=demux_stats)
return qc_objects
def __init__(self, run_dir):
self._run_dir = os.path.normpath(run_dir)
assert os.path.exists(self._run_dir), "The path %s is invalid" % self._run_dir
ss_file = self._find_samplesheet()
if ss_file is not None:
samplesheet = MiSeqSampleSheet(ss_file)
self.samplesheet = samplesheet
parser = FlowcellRunMetricsParser(self._run_dir)
self.run_config = parser.parseRunParameters()
self._fastq = self._fastq_files()
def __init__(self, run_dir, samplesheet=None):
self._run_dir = os.path.normpath(run_dir)
assert os.path.exists(
self._run_dir), "The path %s is invalid" % self._run_dir
# Parse the run parameters
parser = FlowcellRunMetricsParser(self._run_dir)
self.run_config = parser.parseRunParameters()
self.run_info = parser.parseRunInfo()
self.samplesheet_file = samplesheet or IlluminaRun.get_samplesheet(
self._run_dir)
def __init__(self, run_dir):
self._run_dir = os.path.normpath(run_dir)
assert os.path.exists(
self._run_dir), "The path %s is invalid" % self._run_dir
ss_file = self._find_samplesheet()
if ss_file is not None:
samplesheet = MiSeqSampleSheet(ss_file)
self.samplesheet = samplesheet
parser = FlowcellRunMetricsParser(self._run_dir)
self.run_config = parser.parseRunParameters()
self._fastq = self._fastq_files()
def _collect_casava_qc(self):
qc_objects = []
runinfo_csv = os.path.join(os.path.join(self._meta.root_path, self.pargs.flowcell), "{}.csv".format(fc_id(self.pargs.flowcell)))
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")
try:
with open(runinfo_csv) as fh:
runinfo_reader = csv.reader(fh)
runinfo = [x for x in runinfo_reader]
except IOError as e:
self.app.log.warn(str(e))
raise e
fcdir = os.path.join(os.path.abspath(self._meta.root_path), self.pargs.flowcell)
(fc_date, fc_name) = fc_parts(self.pargs.flowcell)
## Check modification time
if modified_within_days(fcdir, self.pargs.mtime):
fc_kw = dict(fc_date = fc_date, fc_name=fc_name)
parser = FlowcellRunMetricsParser(fcdir)
fcobj = FlowcellRunMetricsDocument(fc_date, fc_name)
fcobj["RunInfo"] = parser.parseRunInfo(**fc_kw)
fcobj["RunParameters"] = parser.parseRunParameters(**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"] = parser.parse_samplesheet_csv(runinfo_csv=runinfo_csv, **fc_kw)
qc_objects.append(fcobj)
qc_objects = self._parse_samplesheet(runinfo, qc_objects, fc_date, fc_name, fcdir, demultiplex_stats=fcobj["illumina"]["Demultiplex_Stats"])
return qc_objects
def _collect_pre_casava_qc(self):
qc_objects = []
as_yaml = False
runinfo_csv = os.path.join(
os.path.join(self._meta.root_path, self.pargs.flowcell),
"{}.csv".format(fc_id(self.pargs.flowcell)))
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_yaml = os.path.join(os.path.abspath(self.pargs.flowcell),
"run_info.yaml")
try:
if os.path.exists(runinfo_csv):
with open(runinfo_csv) as fh:
runinfo_reader = csv.reader(fh)
runinfo = [x for x in runinfo_reader]
else:
as_yaml = True
with open(runinfo_yaml) as fh:
runinfo = yaml.load(fh)
except IOError as e:
self.app.log.warn(str(e))
raise e
fcdir = os.path.abspath(self.pargs.flowcell)
(fc_date, fc_name) = fc_parts(self.pargs.flowcell)
## Check modification time
if modified_within_days(fcdir, self.pargs.mtime):
fc_kw = dict(fc_date=fc_date, fc_name=fc_name)
parser = FlowcellRunMetricsParser(fcdir)
fcobj = FlowcellRunMetricsDocument(**fc_kw)
fcobj["RunInfo"] = parser.parseRunInfo(**fc_kw)
fcobj["RunParameters"] = parser.parseRunParameters(**fc_kw)
fcobj["illumina"] = parser.parse_illumina_metrics(fullRTA=False,
**fc_kw)
fcobj["bc_metrics"] = parser.parse_bc_metrics(**fc_kw)
fcobj["filter_metrics"] = parser.parse_filter_metrics(**fc_kw)
fcobj["samplesheet_csv"] = parser.parse_samplesheet_csv(
runinfo_csv=runinfo_csv, **fc_kw)
fcobj["run_info_yaml"] = parser.parse_run_info_yaml(**fc_kw)
qc_objects.append(fcobj)
else:
return qc_objects
qc_objects = self._parse_samplesheet(runinfo,
qc_objects,
fc_date,
fc_name,
fcdir,
as_yaml=as_yaml)
return qc_objects
def collect_metrics(path, log):
parser = FlowcellRunMetricsParser(path)
run_info = parser.parseRunInfo()
fcid = run_info.get('Flowcell',None)
if fcid is None:
log.error("Could not parse flowcell id from RunInfo.xml")
return {}
# Insert a dummy character as the parse method expects a flowcell position
metrics = parser.parse_demultiplex_stats_htm(fcid)
metrics['RunInfo'] = run_info
# Get the undemultiplexed indexes
undemux = parser.parse_undemultiplexed_barcode_metrics(fcid)
metrics['Undemultiplexed'] = undemux
return metrics
def collect_metrics(path):
parser = FlowcellRunMetricsParser(path)
run_info = parser.parseRunInfo()
fcid = run_info.get('Flowcell', None)
if fcid is None:
LOG.error("Could not parse flowcell id from RunInfo.xml")
return {}
# Insert a dummy character as the parse method expects a flowcell position
metrics = parser.parse_demultiplex_stats_htm(fcid)
metrics['RunInfo'] = run_info
# Get the undemultiplexed indexes
undemux = parser.parse_undemultiplexed_barcode_metrics(fcid)
metrics['Undemultiplexed'] = undemux
return metrics
def parse_casava_directory(fc_dir):
"""Traverse a bcl2fastq v2.17 generated directory structure and return a dictionary
"""
projects = []
fc_dir = os.path.abspath(fc_dir)
parser = FlowcellRunMetricsParser(fc_dir)
run_info = parser.parseRunInfo()
runparams = parser.parseRunParameters()
fc_name = run_info.get('Flowcell',None)
fc_date = run_info.get('Date',None)
fc_pos = runparams.get('FCPosition','')
assert fc_name is not None and fc_date is not None, "Could not parse flowcell name and flowcell date"
unaligned_dir_pattern = os.path.join(fc_dir,"{}".format(CASAVA_OUTPUT_DIR))
basecall_stats_dir_pattern = os.path.join(unaligned_dir_pattern,"Basecall_Stats_*")
basecall_stats_dir = [os.path.relpath(d,fc_dir) for d in glob.glob(basecall_stats_dir_pattern)]
project_dir_pattern = os.path.join(unaligned_dir_pattern,"*__*_*_*")
data=read_ssheet_csv(fc_dir)
for project_dir in glob.glob(project_dir_pattern):
project_samples = []
sample_dir_pattern = os.path.join(project_dir,"Sample_*")
for sample_dir in glob.glob(sample_dir_pattern):
fastq_file_pattern = os.path.join(sample_dir,"*.fastq.gz")
fastq_files = [os.path.basename(file) for file in glob.glob(fastq_file_pattern)]
sample_name = os.path.basename(sample_dir).replace("Sample_","").replace('__','.')
samplesheet_pattern = os.path.join(sample_dir, "SampleSheet.csv")
if not os.path.exists(samplesheet_pattern):
write_samplesheet(samplesheet_pattern,data,sample_name,fc_name,fc_dir)
samplesheet = glob.glob(samplesheet_pattern)
project_samples.append({'sample_dir': os.path.basename(sample_dir),
'sample_name': sample_name,
'files': fastq_files,
'samplesheet': os.path.basename(samplesheet[0])})
project_name = os.path.basename(project_dir).replace('__','.')
projects.append({'data_dir': os.path.relpath(os.path.dirname(project_dir),fc_dir),
'project_dir': os.path.basename(project_dir),
'project_name': project_name,
'samples': project_samples})
return {'fc_dir': fc_dir, 'fc_name': '{}{}'.format(fc_pos,fc_name), 'fc_date': fc_date, 'basecall_stats_dir': basecall_stats_dir, 'projects': projects}
def _collect_pre_casava_qc(self):
qc_objects = []
as_yaml = False
read_setup = None
fcdir = os.path.abspath(self.pargs.flowcell)
## Check modification time
if not modified_within_days(fcdir, self.pargs.mtime):
return qc_objects
# 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 len(runinfo) == 0:
runinfo_yaml = os.path.join(os.path.abspath(self.pargs.flowcell), "run_info.yaml")
as_yaml = True
try:
with open(runinfo_yaml) as fh:
runinfo = yaml.load(fh)
except IOError as e:
self.app.log.warn(str(e))
raise e
# 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["illumina"] = parser.parse_illumina_metrics(fullRTA=False, **fc_kw)
fcobj["bc_metrics"] = parser.parse_bc_metrics(**fc_kw)
fcobj["filter_metrics"] = parser.parse_filter_metrics(**fc_kw)
fcobj["samplesheet_csv"] = runinfo
fcobj["run_info_yaml"] = parser.parse_run_info_yaml(**fc_kw)
read_setup = fcobj["RunInfo"].get('Reads',[])
fcobj["run_setup"] = self._run_setup(read_setup)
qc_objects.append(fcobj)
qc_objects = self._parse_samplesheet(runinfo, qc_objects, fc_date, "{}{}".format(fc_pos,fc_name), fcdir, as_yaml=as_yaml, setup=read_setup)
return qc_objects
def parse_casava_directory(fc_dir):
"""Traverse a CASAVA 1.8+ generated directory structure and return a dictionary
"""
projects = []
fc_dir = os.path.abspath(fc_dir)
parser = FlowcellRunMetricsParser(fc_dir)
run_info = parser.parseRunInfo()
runparams = parser.parseRunParameters()
fc_name = run_info.get('Flowcell',None)
fc_date = run_info.get('Date',None)
fc_pos = runparams.get('FCPosition','')
assert fc_name is not None and fc_date is not None, "Could not parse flowcell name and flowcell date"
unaligned_dir_pattern = os.path.join(fc_dir,"{}*".format(CASAVA_OUTPUT_DIR))
basecall_stats_dir_pattern = os.path.join(unaligned_dir_pattern,"Basecall_Stats_*")
basecall_stats_dir = [os.path.relpath(d,fc_dir) for d in glob.glob(basecall_stats_dir_pattern)]
project_dir_pattern = os.path.join(unaligned_dir_pattern,"Project_*")
for project_dir in glob.glob(project_dir_pattern):
project_samples = []
sample_dir_pattern = os.path.join(project_dir,"Sample_*")
for sample_dir in glob.glob(sample_dir_pattern):
fastq_file_pattern = os.path.join(sample_dir,"*.fastq.gz")
samplesheet_pattern = os.path.join(sample_dir,"*.csv")
fastq_files = [os.path.basename(file) for file in glob.glob(fastq_file_pattern)]
samplesheet = glob.glob(samplesheet_pattern)
assert len(samplesheet) == 1, "ERROR: Could not unambiguously locate samplesheet in %s" % sample_dir
sample_name = os.path.basename(sample_dir).replace("Sample_","").replace('__','.')
project_samples.append({'sample_dir': os.path.basename(sample_dir),
'sample_name': sample_name,
'files': fastq_files,
'samplesheet': os.path.basename(samplesheet[0])})
project_name = os.path.basename(project_dir).replace("Project_","").replace('__','.')
projects.append({'data_dir': os.path.relpath(os.path.dirname(project_dir),fc_dir),
'project_dir': os.path.basename(project_dir),
'project_name': project_name,
'samples': project_samples})
return {'fc_dir': fc_dir, 'fc_name': '{}{}'.format(fc_pos,fc_name), 'fc_date': fc_date, 'basecall_stats_dir': basecall_stats_dir, 'projects': projects}
def _collect_pre_casava_qc(self):
qc_objects = []
as_yaml = False
read_setup = None
fcdir = os.path.abspath(self.pargs.flowcell)
## Check modification time
if not modified_within_days(fcdir, self.pargs.mtime):
return qc_objects
# 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 len(runinfo) == 0:
runinfo_yaml = os.path.join(os.path.abspath(self.pargs.flowcell), "run_info.yaml")
as_yaml = True
try:
with open(runinfo_yaml) as fh:
runinfo = yaml.load(fh)
except IOError as e:
self.app.log.warn(str(e))
raise e
# 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["illumina"] = parser.parse_illumina_metrics(fullRTA=False, **fc_kw)
fcobj["bc_metrics"] = parser.parse_bc_metrics(**fc_kw)
fcobj["filter_metrics"] = parser.parse_filter_metrics(**fc_kw)
fcobj["samplesheet_csv"] = runinfo
fcobj["run_info_yaml"] = parser.parse_run_info_yaml(**fc_kw)
read_setup = fcobj["RunInfo"].get('Reads',[])
fcobj["run_setup"] = self._run_setup(read_setup)
qc_objects.append(fcobj)
qc_objects = self._parse_samplesheet(runinfo, qc_objects, fc_date, "{}{}".format(fc_pos,fc_name), fcdir, as_yaml=as_yaml, 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
def _collect_pre_casava_qc(self):
qc_objects = []
as_yaml = False
runinfo_csv = os.path.join(
os.path.join(self._meta.root_path, self.pargs.flowcell), "{}.csv".format(fc_id(self.pargs.flowcell))
)
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_yaml = os.path.join(os.path.abspath(self.pargs.flowcell), "run_info.yaml")
try:
if os.path.exists(runinfo_csv):
with open(runinfo_csv) as fh:
runinfo_reader = csv.reader(fh)
runinfo = [x for x in runinfo_reader]
else:
as_yaml = True
with open(runinfo_yaml) as fh:
runinfo = yaml.load(fh)
except IOError as e:
self.app.log.warn(str(e))
raise e
fcdir = os.path.abspath(self.pargs.flowcell)
(fc_date, fc_name) = fc_parts(self.pargs.flowcell)
## Check modification time
if modified_within_days(fcdir, self.pargs.mtime):
fc_kw = dict(fc_date=fc_date, fc_name=fc_name)
parser = FlowcellRunMetricsParser(fcdir)
fcobj = FlowcellRunMetricsDocument(**fc_kw)
fcobj["RunInfo"] = parser.parseRunInfo(**fc_kw)
fcobj["RunParameters"] = parser.parseRunParameters(**fc_kw)
fcobj["illumina"] = parser.parse_illumina_metrics(fullRTA=False, **fc_kw)
fcobj["bc_metrics"] = parser.parse_bc_metrics(**fc_kw)
fcobj["filter_metrics"] = parser.parse_filter_metrics(**fc_kw)
fcobj["samplesheet_csv"] = parser.parse_samplesheet_csv(runinfo_csv=runinfo_csv, **fc_kw)
fcobj["run_info_yaml"] = parser.parse_run_info_yaml(**fc_kw)
qc_objects.append(fcobj)
else:
return qc_objects
qc_objects = self._parse_samplesheet(runinfo, qc_objects, fc_date, fc_name, fcdir, as_yaml=as_yaml)
return qc_objects
def test_parse_demux_stats(self):
"""Test parsing of a Demultiplex_Stats.htm file"""
parser = FlowcellRunMetricsParser(self.fcdir)
data = parser.parse_demultiplex_stats_htm(**self.fc_kw)
self.assertEqual(data['Barcode_lane_statistics'][0]['# Reads'],
'39,034,396')
def test_parseRunParameters(self):
parser = FlowcellRunMetricsParser(self.fcdir)
data = parser.parseRunParameters(**self.fc_kw)
self.assertEqual(data['Setup']['FPGADynamicFocusSettings']['CVGainPosLocked'],'500')
self.assertEqual(data['Setup']['Reads']['Read'][0]['NumCycles'],'101')
self.assertEqual(data['Setup']['SelectedSections']['Section'][1]['Name'],'B_1')
def test_parse_demux_stats(self):
"""Test parsing of a Demultiplex_Stats.htm file"""
parser = FlowcellRunMetricsParser(self.fcdir)
data = parser.parse_demultiplex_stats_htm(**self.fc_kw)
self.assertEqual(data["Barcode_lane_statistics"][0]["# Reads"], "39,034,396")
def test_parseRunParameters(self):
parser = FlowcellRunMetricsParser(self.fcdir)
data = parser.parseRunParameters(**self.fc_kw)
self.assertEqual(data["Setup"]["FPGADynamicFocusSettings"]["CVGainPosLocked"], "500")
self.assertEqual(data["Setup"]["Reads"]["Read"][0]["NumCycles"], "101")
self.assertEqual(data["Setup"]["SelectedSections"]["Section"][1]["Name"], "B_1")