def addAnalysisMetrics(beadMetrics, BaseCallerMetrics, res):
#print 'addAnalysisMetrics'
analysis_metrics_map = {
'libLive': 0,
'libKp': 0,
'libFinal': 0,
'tfLive': 0,
'tfKp': 0,
'tfFinal': 0,
'lib_pass_basecaller': 0,
'lib_pass_cafie': 0,
'empty': 0,
'bead': 0,
'live': 0,
'dud': 0,
'amb': 0,
'tf': 0,
'lib': 0,
'pinned': 0,
'ignored': 0,
'excluded': 0,
'washout': 0,
'washout_dud': 0,
'washout_ambiguous': 0,
'washout_live': 0,
'washout_test_fragment': 0,
'washout_library': 0,
'keypass_all_beads': 0,
'sysCF': 0.0,
'sysIE': 0.0,
'sysDR': 0.0,
'libFinal': 0,
'tfFinal': 0,
}
bead_metrics_map = {
'empty': 'Empty Wells',
'bead': 'Bead Wells',
'live': 'Live Beads',
'dud': 'Dud Beads',
'amb': 'Ambiguous Beads',
'tf': 'Test Fragment Beads',
'lib': 'Library Beads',
'pinned': 'Pinned Wells',
'ignored': 'Ignored Wells',
'excluded': 'Excluded Wells',
'washout': 'Washout Wells',
'washout_dud': 'Washout Dud',
'washout_ambiguous': 'Washout Ambiguous',
'washout_live': 'Washout Live',
'washout_test_fragment': 'Washout Test Fragment',
'washout_library': 'Washout Library',
'keypass_all_beads': 'Keypass Beads'
}
kwargs = {
'report': res,
'libMix': 0,
'tfMix': 0,
'sysCF': 0.0,
'sysIE': 0.0,
'sysDR': 0.0
}
if BaseCallerMetrics:
try:
analysis_metrics_map["libFinal"] = BaseCallerMetrics["Filtering"][
"ReadDetails"]["lib"]["valid"]
analysis_metrics_map["tfFinal"] = BaseCallerMetrics["Filtering"][
"ReadDetails"]["tf"]["valid"]
except Exception as err:
print(
"During AnalysisMetrics creation, reading from BaseCaller.json: %s",
err)
kwargs.update(analysis_metrics_map)
if beadMetrics:
for dbname, key in bead_metrics_map.iteritems():
kwargs[dbname] = set_type(beadMetrics.get(key, 0))
if BaseCallerMetrics:
try:
kwargs['sysCF'] = 100.0 * BaseCallerMetrics['Phasing']['CF']
kwargs['sysIE'] = 100.0 * BaseCallerMetrics['Phasing']['IE']
kwargs['sysDR'] = 100.0 * BaseCallerMetrics['Phasing']['DR']
except Exception as err:
print(
"During AnalysisMetrics creation, reading from BaseCaller.json: %s",
err)
analysismetrics = res.analysismetrics or models.AnalysisMetrics()
for key, value in kwargs.items():
setattr(analysismetrics, key, value)
analysismetrics.save()
res.analysismetrics = analysismetrics
res.save()
def addAnalysisMetrics(beadMetrics, BaseCallerMetrics, res):
# print 'addAnalysisMetrics'
kwargs = {
"report": res,
"libLive": 0,
"libKp": 0,
"libFinal": 0,
"tfLive": 0,
"tfKp": 0,
"tfFinal": 0,
"lib_pass_basecaller": 0,
"lib_pass_cafie": 0,
"empty": 0,
"bead": 0,
"live": 0,
"dud": 0,
"amb": 0,
"tf": 0,
"lib": 0,
"pinned": 0,
"ignored": 0,
"excluded": 0,
"washout": 0,
"washout_dud": 0,
"washout_ambiguous": 0,
"washout_live": 0,
"washout_test_fragment": 0,
"washout_library": 0,
"keypass_all_beads": 0,
"sysCF": 0.0,
"sysIE": 0.0,
"sysDR": 0.0,
"libFinal": 0,
"tfFinal": 0,
"libMix": 0,
"tfMix": 0,
"total": 0,
"adjusted_addressable": 0,
"loading": 0.0,
}
bead_metrics_map = {
"empty": "Empty Wells",
"bead": "Bead Wells",
"live": "Live Beads",
"dud": "Dud Beads",
"amb": "Ambiguous Beads",
"tf": "Test Fragment Beads",
"lib": "Library Beads",
"pinned": "Pinned Wells",
"ignored": "Ignored Wells",
"excluded": "Excluded Wells",
"washout": "Washout Wells",
"washout_dud": "Washout Dud",
"washout_ambiguous": "Washout Ambiguous",
"washout_live": "Washout Live",
"washout_test_fragment": "Washout Test Fragment",
"washout_library": "Washout Library",
"keypass_all_beads": "Keypass Beads",
"total": "Total Wells",
"adjusted_addressable": "Adjusted Addressable Wells",
}
if BaseCallerMetrics:
try:
kwargs["libFinal"] = BaseCallerMetrics["Filtering"]["ReadDetails"][
"lib"]["valid"]
kwargs["tfFinal"] = BaseCallerMetrics["Filtering"]["ReadDetails"][
"tf"]["valid"]
except Exception as err:
print(
"During AnalysisMetrics creation, reading from BaseCaller.json: %s",
err)
if beadMetrics:
for dbname, key in bead_metrics_map.items():
kwargs[dbname] = set_type(beadMetrics.get(key, 0))
if not kwargs["adjusted_addressable"]:
kwargs[
"adjusted_addressable"] = kwargs["total"] - kwargs["excluded"]
if kwargs["adjusted_addressable"]:
kwargs["loading"] = (100 * float(kwargs["bead"]) /
kwargs["adjusted_addressable"])
if BaseCallerMetrics:
try:
kwargs["sysCF"] = 100.0 * BaseCallerMetrics["Phasing"]["CF"]
kwargs["sysIE"] = 100.0 * BaseCallerMetrics["Phasing"]["IE"]
kwargs["sysDR"] = 100.0 * BaseCallerMetrics["Phasing"]["DR"]
except Exception as err:
print(
"During AnalysisMetrics creation, reading from BaseCaller.json: %s",
err)
analysismetrics = res.analysismetrics or models.AnalysisMetrics()
for key, value in list(kwargs.items()):
setattr(analysismetrics, key, value)
analysismetrics.save()
res.analysismetrics = analysismetrics
res.save()