def loadReferenceAndModel(self, referencePath, cmpH5Path):
# Load the reference contigs - annotated with their refID from the cmp.h5
contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path)
# Read reference info table from cmp.h5
(refInfoTable, _) = ReferenceUtils.loadCmpH5Tables(cmpH5Path)
self.refInfo = refInfoTable
# There are three different ways the ipdModel can be loaded.
# In order of precedence they are:
# 1. Explicit path passed to --ipdModel
# 2. Path to parameter bundle, model selected using the cmp.h5's chemistry info
# 3. Fall back to built-in model.
# By default, use built-in model
ipdModel = None
if self.args.ipdModel:
ipdModel = self.args.ipdModel
logging.info("Using passed in ipd model: %s" % self.args.ipdModel)
if not os.path.exists(self.args.ipdModel):
logging.error("Couldn't find model file: %s" %
self.args.ipdModel)
elif self.args.paramsPath:
if not os.path.exists(self.args.paramsPath):
logging.error("Params path doesn't exist: %s" %
self.args.paramsPath)
sys.exit(1)
majorityChem = ReferenceUtils.loadCmpH5Chemistry(cmpH5Path)
ipdModel = os.path.join(self.args.paramsPath, majorityChem + ".h5")
if majorityChem == 'unknown':
logging.warning(
"Chemistry is unknown. Falling back to built-in model")
ipdModel = None
elif not os.path.exists(ipdModel):
logging.warning("Model not found: %s" % ipdModel)
logging.warning("Falling back to built-in model")
ipdModel = None
else:
logging.info("Using Chemistry matched IPD model: %s" %
ipdModel)
self.ipdModel = IpdModel(contigs, ipdModel, self.args.modelIters)
def loadReferenceAndModel(self, referencePath, cmpH5Path):
# Load the reference contigs - annotated with their refID from the cmp.h5
contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path)
# Read reference info table from cmp.h5
(refInfoTable, _) = ReferenceUtils.loadCmpH5Tables(cmpH5Path)
self.refInfo = refInfoTable
# There are three different ways the ipdModel can be loaded.
# In order of precedence they are:
# 1. Explicit path passed to --ipdModel
# 2. Path to parameter bundle, model selected using the cmp.h5's chemistry info
# 3. Fall back to built-in model.
# By default, use built-in model
ipdModel = None
if self.args.ipdModel:
ipdModel = self.args.ipdModel
logging.info("Using passed in ipd model: %s" % self.args.ipdModel)
if not os.path.exists(self.args.ipdModel):
logging.error("Couldn't find model file: %s" % self.args.ipdModel)
elif self.args.paramsPath:
if not os.path.exists(self.args.paramsPath):
logging.error("Params path doesn't exist: %s" % self.args.paramsPath)
sys.exit(1)
majorityChem = ReferenceUtils.loadCmpH5Chemistry(cmpH5Path)
ipdModel = os.path.join(self.args.paramsPath, majorityChem + ".h5")
if majorityChem == "unknown":
logging.warning("Chemistry is unknown. Falling back to built-in model")
ipdModel = None
elif not os.path.exists(ipdModel):
logging.warning("Model not found: %s" % ipdModel)
logging.warning("Falling back to built-in model")
ipdModel = None
else:
logging.info("Using Chemistry matched IPD model: %s" % ipdModel)
self.ipdModel = IpdModel(contigs, ipdModel, self.args.modelIters)
def loadReferenceAndModel(self, referencePath, cmpH5Path):
# Load the reference contigs - annotated with their refID from the cmp.h5
contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path)
# Read reference info table from cmp.h5
(refInfoTable, _) = ReferenceUtils.loadCmpH5Tables(cmpH5Path)
if (self.options.refContigs is not None
or self.options.refContigIndex != -1):
if (self.options.refContigs is not None
and self.options.refContigIndex != -1):
requestedIds = set(self.options.refContigs.split(',')).union(
[self.options.refContigIndex])
elif (self.options.refContigs is None
and self.options.refContigIndex != -1):
requestedIds = set([self.options.refContigIndex])
elif (self.options.refContigs is not None
and self.options.refContigIndex == -1):
requestedIds = set(self.options.refContigs.split(','))
relevantContigs = [
i for (i, rec) in enumerate(refInfoTable)
if (rec.FullName in requestedIds or rec.Name in requestedIds
or rec.RefInfoID in requestedIds)
]
self.refInfo = refInfoTable[relevantContigs]
else:
self.refInfo = refInfoTable
# There are three different ways the ipdModel can be loaded.
# In order of precedence they are:
# 1. Explicit path passed to --ipdModel
# 2. Path to parameter bundle, model selected using the cmp.h5's sequencingChemistry tags
# 3. Fall back to built-in model.
# By default, use built-in model
ipdModel = None
if self.args.ipdModel:
ipdModel = self.args.ipdModel
logging.info("Using passed in ipd model: %s" % self.args.ipdModel)
if not os.path.exists(self.args.ipdModel):
logging.error("Couldn't find model file: %s" %
self.args.ipdModel)
sys.exit(1)
elif self.args.paramsPath:
if not os.path.exists(self.args.paramsPath):
logging.error("Params path doesn't exist: %s" %
self.args.paramsPath)
sys.exit(1)
majorityChem = ReferenceUtils.loadCmpH5Chemistry(cmpH5Path)
ipdModel = os.path.join(self.args.paramsPath, majorityChem + ".h5")
if majorityChem == 'unknown':
logging.error(
"Chemistry cannot be identified---cannot perform kinetic analysis"
)
sys.exit(1)
elif not os.path.exists(ipdModel):
logging.error(
"Aborting, no kinetics model available for this chemistry: %s"
% ipdModel)
sys.exit(1)
else:
logging.info("Using Chemistry matched IPD model: %s" %
ipdModel)
self.ipdModel = IpdModel(contigs, ipdModel, self.args.modelIters)
def loadReferenceAndModel(self, referencePath, cmpH5Path):
# Load the reference contigs - annotated with their refID from the cmp.h5
contigs = ReferenceUtils.loadReferenceContigs(referencePath, cmpH5Path)
# Read reference info table from cmp.h5
(refInfoTable, _) = ReferenceUtils.loadCmpH5Tables(cmpH5Path)
if (self.options.refContigs is not None or
self.options.refContigIndex != -1):
if (self.options.refContigs is not None and
self.options.refContigIndex != -1):
requestedIds = set(self.options.refContigs.split(',')).union([self.options.refContigIndex])
elif (self.options.refContigs is None and
self.options.refContigIndex != -1):
requestedIds = set([self.options.refContigIndex])
elif (self.options.refContigs is not None and
self.options.refContigIndex == -1):
requestedIds = set(self.options.refContigs.split(','))
relevantContigs = [ i for (i, rec) in enumerate(refInfoTable)
if (rec.FullName in requestedIds or
rec.Name in requestedIds or
rec.RefInfoID in requestedIds) ]
self.refInfo = refInfoTable[relevantContigs]
else:
self.refInfo = refInfoTable
# There are three different ways the ipdModel can be loaded.
# In order of precedence they are:
# 1. Explicit path passed to --ipdModel
# 2. Path to parameter bundle, model selected using the cmp.h5's sequencingChemistry tags
# 3. Fall back to built-in model.
# By default, use built-in model
ipdModel = None
if self.args.ipdModel:
ipdModel = self.args.ipdModel
logging.info("Using passed in ipd model: %s" % self.args.ipdModel)
if not os.path.exists(self.args.ipdModel):
logging.error("Couldn't find model file: %s" % self.args.ipdModel)
sys.exit(1)
elif self.args.paramsPath:
if not os.path.exists(self.args.paramsPath):
logging.error("Params path doesn't exist: %s" % self.args.paramsPath)
sys.exit(1)
majorityChem = ReferenceUtils.loadCmpH5Chemistry(cmpH5Path)
ipdModel = os.path.join(self.args.paramsPath, majorityChem + ".h5")
if majorityChem == 'unknown':
logging.warning("Chemistry is unknown. Falling back to built-in model")
ipdModel = None
elif not os.path.exists(ipdModel):
logging.warning("Model not found: %s" % ipdModel)
logging.warning("Falling back to built-in model")
ipdModel = None
else:
logging.info("Using Chemistry matched IPD model: %s" % ipdModel)
self.ipdModel = IpdModel(contigs, ipdModel, self.args.modelIters)