def _buildParameterSet(parameterSetName, nameValuePairs):
chem, modelName = parameterSetName.split(".")[:2]
if modelName == "AllQVsModel": model = AllQVsModel
elif modelName == "NoMergeQVModel": model = NoMergeQVModel
elif modelName == "NoQVsModel": model = NoQVsModel
elif modelName == "AllQVsMergingByChannelModel": model = AllQVsMergingByChannelModel
elif modelName == "NoQVsMergingByChannelModel": model = NoQVsMergingByChannelModel
else:
logging.error("Found parameter set for unrecognized model: %s" % modelName)
return None
if map(fst, nameValuePairs) != model.parameterNames:
die("Malformed parameter set file")
qvModelParams = cc.QvModelParams(chem, modelName,
*[ float(snd(pair)) for pair in nameValuePairs ])
#
# Dirty hack for --diploid support, diploid model is scaled
# differently. Needs further work.
#
if parameterSetName == "unknown.NoQVsModel":
bandingOptions = cc.BandingOptions(4, 24)
fastScoreThreshold = -50
else:
bandingOptions = cc.BandingOptions(4, 6)
fastScoreThreshold = -12.5
quiverConfig = cc.QuiverConfig(qvModelParams,
cc.ALL_MOVES,
bandingOptions,
fastScoreThreshold)
return ParameterSet(parameterSetName, model, chem, quiverConfig)
def _buildParameterSet(parameterSetName, nameValuePairs):
chem, modelName = parameterSetName.split(".")[:2]
if modelName == "AllQVsModel": model = AllQVsModel
elif modelName == "NoMergeQVModel": model = NoMergeQVModel
elif modelName == "NoQVsModel": model = NoQVsModel
elif modelName == "AllQVsMergingByChannelModel":
model = AllQVsMergingByChannelModel
elif modelName == "NoQVsMergingByChannelModel":
model = NoQVsMergingByChannelModel
else:
logging.error("Found parameter set for unrecognized model: %s" %
modelName)
return None
if map(fst, nameValuePairs) != model.parameterNames:
die("Malformed parameter set file")
qvModelParams = cc.QvModelParams(
chem, modelName, *[float(snd(pair)) for pair in nameValuePairs])
#
# Dirty hack for --diploid support, diploid model is scaled
# differently. Needs further work.
#
if parameterSetName == "unknown.NoQVsModel":
bandingOptions = cc.BandingOptions(4, 24)
fastScoreThreshold = -50
else:
bandingOptions = cc.BandingOptions(4, 6)
fastScoreThreshold = -12.5
quiverConfig = cc.QuiverConfig(qvModelParams, cc.ALL_MOVES, bandingOptions,
fastScoreThreshold)
return ParameterSet(parameterSetName, model, chem, quiverConfig)