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, movieInfoTable) = 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 /MovieInfo/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)
# Use the SequencingChemistry data to select an ipd model
if 'SequencingChemistry' in movieInfoTable.dtype.fields.keys():
# Pick majority chemistry
chemistries = movieInfoTable.SequencingChemistry.tolist()
chemCounts = dict([ (k, len(list(v))) for (k, v) in itertools.groupby(chemistries)])
majorityChem = max(chemCounts, key=chemCounts.get)
# Find the appropriate model file:
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 setUp(self):
# Load the lambda genome from our sample data
dataDir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data')
ref = os.path.join(dataDir, 'lambda', 'sequence', 'lambda.fasta')
cmpFile = os.path.join(dataDir, "p4-c2-lambda-mod-decode.cmp.h5")
self.contigs = ReferenceUtils.loadReferenceContigs(ref, cmpFile)
self.ipdModel = IpdModel(self.contigs)
# Create a functional KineticWorker object that can be poked at manually.
self.kw = KineticWorker(self.ipdModel)
self.cmpH5 = CmpH5Reader(cmpFile)
# Put in our cmp.h5 - this is normally supplied by the Worker superclass
self.kw.caseCmpH5 = self.cmpH5
self.kw.controlCmpH5 = None
self.kw.options = self.getOpts()
