def main():
#Parse the inputs args/options
parser = OptionParser(usage="usage: inputSamFile referenceFastaFile outputVcfFile [options]",
version="%prog 0.1")
#Options
parser.add_option("--noMargin", dest="noMargin", help="Do not marginalise over the read \
alignments, rather use the input alignment to call the variants (this will be faster)",
default=False, action="store_true")
parser.add_option("--alignmentModel", default=os.path.join(pathToBaseNanoporeDir(),
"src", "margin", "mappers", "last_hmm_20.txt"),
help="The model to use in realigning the reads to the reference.")
parser.add_option("--errorModel", default=os.path.join(pathToBaseNanoporeDir(),
"src", "margin", "mappers", "last_hmm_20.txt"),
help="The model to use in calculating the difference between the predicted true reference and the reads.")
parser.add_option("--maxAlignmentLengthPerJob", default=7000000,
help="Maximum total alignment length of alignments to include in one posterior prob calculation job.",
type=int)
parser.add_option("--threshold", default=0.3,
help="The posterior probability threshold for a non-reference base above which to report a variant.",
type=float)
#Add the jobTree options
Stack.addJobTreeOptions(parser)
#Parse the options/arguments
options, args = parser.parse_args()
#Setup logging
setLoggingFromOptions(options)
#Print help message if no input
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
#Exit if the arguments are not what we expect
if len(args) != 3:
raise RuntimeError("Expected three arguments, got: %s" % " ".join(args))
print options.errorModel
print options.threshold
#This line invokes jobTree
i = Stack(Target.makeTargetFn(fn=marginCallerTargetFn, args=(args[0], args[1], args[2], options))).startJobTree(options)
#The return value of the jobtree script is the number of failed jobs. If we have any then
#report this.
if i != 0:
raise RuntimeError("Got failed jobs")
def main():
#Parse the inputs args/options
parser = OptionParser(usage="usage: inputFastqFile referenceFastaFile outputSamFile [options]",
version="%prog 0.1")
#Options
parser.add_option("--em", dest="em",
help="Run expectation maximisation (EM)",
default=False, action="store_true")
##Most people would not want to use the following, but I put them here for debug purposes
parser.add_option("--bwa", dest="bwa", help="Use BWA instead of LAST",
default=False, action="store_true")
parser.add_option("--graphmap", dest="graphmap", help="Use GraphMap instead of LAST",
default=False, action="store_true")
parser.add_option("--graphmapanchor", dest="graphmapanchor", help="Use GraphMap with anchor alignment instead of LAST",
default=False, action="store_true")
parser.add_option("--noRealign", dest="noRealign", help="Don't run any realignment step",
default=False, action="store_true")
parser.add_option("--noChain", dest="noChain", help="Don't run any chaining step",
default=False, action="store_true")
parser.add_option("--gapGamma", dest="gapGamma", help="Set the gap gamma for the AMAP function",
default=0.5, type=float)
parser.add_option("--matchGamma", dest="matchGamma", help="Set the match gamma for the AMAP function",
default=0.0, type=float)
#Add the cPecan expectation maximisation options
options = cPecan.cPecanEm.Options()
options.inputModel = os.path.join(pathToBaseNanoporeDir(), "src", "margin", "mappers", "last_hmm_20.txt")
options.modelType="fiveStateAsymmetric" #"threeStateAsymmetric"
options.optionsToRealign="--diagonalExpansion=10 --splitMatrixBiggerThanThis=300"
options.randomStart = True
options.trials = 3
options.outputTrialHmms = True
options.iterations = 100
options.maxAlignmentLengthPerJob=700000
options.maxAlignmentLengthToSample = 50000000
#options.outputXMLModelFile = outputModel + ".xml"
#options.updateTheBand = True
#options.useDefaultModelAsStart = True
#options.setJukesCantorStartingEmissions=0.3
options.trainEmissions=True
#options.tieEmissions = True
addExpectationMaximisationOptions(parser, options)
#Add the jobTree options
Stack.addJobTreeOptions(parser)
#Parse the options/arguments
options, args = parser.parse_args()
#Setup logging
setLoggingFromOptions(options)
#Print help message if no input
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
#Exit if the arguments are not what we expect
if len(args) != 3:
raise RuntimeError("Expected three arguments, got: %s" % " ".join(args))
#Set the mapper
if options.noRealign:
if options.noChain: # i.e. --noChain --noRealign
# mapper = Bwa if options.bwa else Last
mapper = Last;
if (options.bwa):
mapper = Bwa;
if (options.graphmap):
mapper = GraphMap;
if (options.graphmapanchor):
mapper = GraphMapAnchor;
else: # i.e. --noRealign
# mapper = BwaChain if options.bwa else LastChain
mapper = LastChain;
if (options.bwa):
mapper = BwaChain;
if (options.graphmap):
mapper = GraphMapChain;
if (options.graphmapanchor):
mapper = GraphMapAnchorChain;
else:
# mapper = BwaRealign if options.bwa else LastRealign
mapper = LastRealign;
if (options.bwa):
mapper = BwaRealign;
if (options.graphmap):
mapper = GraphMapRealign;
if (options.graphmapanchor):
mapper = GraphMapAnchorRealign;
#This line invokes jobTree
i = Stack(mapper(readFastqFile=args[0], referenceFastaFile=args[1], outputSamFile=args[2],
options=options)).startJobTree(options)
#The return value of the jobtree script is the number of failed jobs. If we have any then
#report this.
if i != 0:
raise RuntimeError("Got failed jobs")
def getFile(self, file):
return os.path.join(pathToBaseNanoporeDir(), file)
def main():
#Parse the inputs args/options
parser = OptionParser(usage="usage: inputFastqFile referenceFastaFile outputSamFile [options]",
version="%prog 0.1")
#Options
parser.add_option("--em", dest="em",
help="Run expectation maximisation (EM)",
default=False, action="store_true")
##Most people would not want to use the following, but I put them here for debug purposes
parser.add_option("--bwa", dest="bwa", help="Use BWA instead of LAST",
default=False, action="store_true")
parser.add_option("--noRealign", dest="noRealign", help="Don't run any realignment step",
default=False, action="store_true")
parser.add_option("--noChain", dest="noChain", help="Don't run any chaining step",
default=False, action="store_true")
parser.add_option("--gapGamma", dest="gapGamma", help="Set the gap gamma for the AMAP function",
default=0.5, type=float)
parser.add_option("--matchGamma", dest="matchGamma", help="Set the match gamma for the AMAP function",
default=0.0, type=float)
#Add the cPecan expectation maximisation options
options = cPecan.cPecanEm.Options()
options.inputModel = os.path.join(pathToBaseNanoporeDir(), "src", "margin", "mappers", "last_hmm_20.txt")
options.modelType="fiveStateAsymmetric" #"threeStateAsymmetric"
options.optionsToRealign="--diagonalExpansion=10 --splitMatrixBiggerThanThis=300"
options.randomStart = True
options.trials = 3
options.outputTrialHmms = True
options.iterations = 100
options.maxAlignmentLengthPerJob=700000
options.maxAlignmentLengthToSample = 50000000
#options.outputXMLModelFile = outputModel + ".xml"
#options.updateTheBand = True
#options.useDefaultModelAsStart = True
#options.setJukesCantorStartingEmissions=0.3
options.trainEmissions=True
#options.tieEmissions = True
addExpectationMaximisationOptions(parser, options)
#Add the jobTree options
Stack.addJobTreeOptions(parser)
#Parse the options/arguments
options, args = parser.parse_args()
#Setup logging
setLoggingFromOptions(options)
#Print help message if no input
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
#Exit if the arguments are not what we expect
if len(args) != 3:
raise RuntimeError("Expected three arguments, got: %s" % " ".join(args))
#Set the mapper
if options.noRealign:
if options.noChain: # i.e. --noChain --noRealign
mapper = Bwa if options.bwa else Last
else: # i.e. --noRealign
mapper = BwaChain if options.bwa else LastChain
else:
mapper = BwaRealign if options.bwa else LastRealign
#This line invokes jobTree
i = Stack(mapper(readFastqFile=args[0], referenceFastaFile=args[1], outputSamFile=args[2],
options=options)).startJobTree(options)
#The return value of the jobtree script is the number of failed jobs. If we have any then
#report this.
if i != 0:
raise RuntimeError("Got failed jobs")
def getFile(self, file):
return os.path.join(pathToBaseNanoporeDir(), file)