def parseArgs():
parser = argparse.ArgumentParser(description='')
parser.add_argument('inputFile',
metavar='copynumberFile',
action='store',
type=utility.existingFile,
help='')
parser.add_argument('iteration',
metavar='iteration',
action='store',
type=int,
help='')
parser.add_argument('-o',
'--output',
dest='outputFolder',
action='store',
type=utility.existingDirectory,
required=False,
default=utility.workingDirectory(),
help='Output folder')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(
description=
'Filter out segments with a medium coverage less than a minum value')
parser.add_argument('inputFile',
metavar='annotedFile',
action='store',
type=utility.existingFile,
help='Input file from annoteSegments.py')
parser.add_argument('-c',
'--control',
dest='controlFile',
action='store',
type=utility.existingFile,
required=True,
help='Control bam file')
parser.add_argument('-t',
'--tumor',
dest='tumoralFile',
action='store',
type=utility.existingFile,
required=True,
help='Tumoral bam file')
parser.add_argument('-b',
'--bed-file',
dest='bedFile',
action='store',
type=utility.existingFile,
required=True,
help='Bed file')
parser.add_argument('-r',
'--reference',
dest='refFile',
action='store',
type=utility.existingFile,
required=True,
help='Reference file')
parser.add_argument('-o',
'--output',
dest='outputFile',
action='store',
type=utility.existingFilePath,
required=False,
default=utility.workingDirectory() +
'/output.coverage.tsv',
help='Output file name')
parser.add_argument('-m',
'--min-coverage',
dest='minCov',
action='store',
type=int,
required=False,
default=25,
help='Minimum coverage value for filter out segments')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(
description=
'Annote segments from mergeSegments.py using a reference file. It discard "Neutral" segments and segments that don\'t intersect any exon'
)
parser.add_argument('inputFile',
metavar='mergedFile',
action='store',
type=utility.existingFile,
help='Input file from mergeSegments.py')
parser.add_argument('-o',
'--output',
dest='outputFile',
action='store',
type=utility.existingFilePath,
required=False,
default=utility.workingDirectory() +
'/output.annotated.tsv',
help='Output file name')
parser.add_argument('-r',
'--ref-annotation',
dest='annotationFile',
action='store',
type=utility.existingFile,
required=False,
default=utility.programDirectory() +
'/refs/genesReference.tsv',
help='Reference file for annotation')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(description='')
parser.add_argument('inputFiles',
metavar='copyCalls',
action='store',
type=utility.getFiles,
help='')
parser.add_argument('threshold',
metavar='threshold',
action='store',
type=int,
help='')
parser.add_argument('-n',
'--patient-id',
dest='patientId',
action='store',
type=str,
required=True,
help='')
parser.add_argument('-o',
'--output',
dest='outputFile',
action='store',
type=utility.existingFilePath,
required=False,
default=utility.workingDirectory() +
'/output.cumulative.tsv',
help='')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(description='') #Add program description
parser.add_argument('configFile',
metavar='configuation-file',
action='store',
type=utility.existingFile,
help='') #Add argument description
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(description = '')
parser.add_argument('inputFiles', metavar = 'filesList',
action='store', nargs='*', type=utility.existingFile,
help='Input file from mergeSegments.py')
parser.add_argument('-o', '--output', dest='outputFile',
action='store', type=utility.existingFilePath, required=False,
default=utility.workingDirectory() + '/output.cumulative.csv',
help='Output file name')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(description = 'Filter the annoteSegments.py or coverageFilter.py output with a given list of genes of interest')
parser.add_argument('inputFile', metavar='inputFile',
action='store', type=utility.existingFile,
help='annoteSegments.py or coverageFilter.py output file')
parser.add_argument('-o', '--output', dest='outputFile',
action='store', type=utility.existingFilePath, required=False,
default=utility.workingDirectory() + '/output.cancer.tsv',
help='Output file name')
parser.add_argument('-r', '--gene-file', dest='geneFile',
action='store', type=utility.existingFile, required=False,
default=utility.programDirectory() + '/refs/cancerGenes.tsv',
help='A reference file with a list of genes of interest')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(
description='Merge segments from R output')
parser.add_argument('inputFile',
metavar='segmentFile',
action='store',
type=utility.existingFile,
help='')
parser.add_argument('-o',
'--output',
dest='outputFile',
action='store',
type=utility.existingFilePath,
required=False,
default=utility.workingDirectory() +
'/output.merged.tsv',
help='')
parser.add_argument('-r',
'--ref-arm',
dest='armRef',
action='store',
type=utility.existingFile,
required=False,
default=utility.programDirectory() +
'/refs/armSize.tsv',
help='')
parser.add_argument('-a',
'--amp-threshold',
dest='maximum',
action='store',
type=float,
required=False,
default=0.25,
help='')
parser.add_argument('-d',
'--del-threshold',
dest='minimum',
action='store',
type=float,
required=False,
default=-0.25,
help='')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs(): #TODO: improve descriptions
parser = argparse.ArgumentParser(
description=
'Use Samtools and VarScan to create an output file for copy number variation study'
)
parser.add_argument('controlFile',
metavar='controlBam',
action='store',
type=utility.existingFile,
help='Bam file for control samples, with index')
parser.add_argument('tumoralFile',
metavar='tumoralBam',
action='store',
type=utility.existingFile,
help='Bam file for tumoral samples, with index')
parser.add_argument('-r',
'--reference',
dest='refFile',
action='store',
type=utility.existingFile,
required=True,
help='Indexed reference file')
parser.add_argument('-o',
'--output',
dest='outputFolder',
action='store',
type=utility.existingDirectory,
required=False,
default=utility.workingDirectory(),
help='Output folder')
parser.add_argument('-b',
'--bed',
dest='bedFile',
action='store',
type=utility.existingFile,
required=False,
help='Bed file')
args = parser.parse_args()
utility.printParameters(args)
return args
def parseArgs():
parser = argparse.ArgumentParser(description='')
parser.add_argument('inputDir',
metavar='copyCallsDir',
action='store',
type=utility.existingDirectory,
help='')
parser.add_argument('-o',
'--output',
dest='outputFile',
action='store',
type=utility.existingFilePath,
required=False,
default=utility.workingDirectory() +
'/copyCalls.summary.tsv',
help='')
args = parser.parse_args()
utility.printParameters(args)
return args