def ucsc_illuminaga_dnaseq_cont_automated(inDir, outDir, cancer, flog, REALRUN): print cancer, sys._getframe().f_code.co_name distribution = False PATHPATTERN = "IlluminaGA_DNASeq_Cont_automated." PLATFORM = "IlluminaGA" suffix = "ucsc" namesuffix = "mutation_ucsc_maf_gene" dataProducer = "University of Californis Santa Cruz GDAC" clean = 1 mafToMatrix(inDir, outDir, cancer, flog, PATHPATTERN, suffix, namesuffix, dataProducer, REALRUN, clean, PLATFORM, distribution) clean = 0 namesuffix = "mutation_ucsc_maf" mafToXena(inDir, outDir, cancer, flog, PATHPATTERN, suffix, namesuffix, dataProducer, REALRUN, clean, PLATFORM, distribution) clean = 0 namesuffix = "mutation_ucsc_vcf" type = "somatic" radia.radiaToXena(inDir, outDir, cancer, flog, PATHPATTERN, suffix, namesuffix, dataProducer, REALRUN, clean, PLATFORM, distribution, type)
def germline_ucsc_illuminaga_dnaseq_cont (inDir, outDir, cancer,flog,REALRUN): print cancer, sys._getframe().f_code.co_name distribution= False PATHPATTERN= "IlluminaGA_DNASeq_Cont." PLATFORM = "IlluminaGA" suffix = "ucsc" namesuffix = "germline_ucsc_vcf" dataProducer = "University of Californis Santa Cruz GDAC" clean=0 type ="germline" radia.radiaToXena (inDir, outDir, cancer,flog, PATHPATTERN, suffix, namesuffix, dataProducer,REALRUN,clean, PLATFORM,distribution, type)
def ucsc_solid_dnaseq_cont (inDir, outDir, cancer,flog,REALRUN): print cancer, sys._getframe().f_code.co_name distribution = True PATHPATTERN= "SOLiD_DNASeq_Cont." PLATFORM = "SOLiD" suffix = "ucsc" namesuffix = "mutation_ucsc_solid_gene_maf" dataProducer = "University of Californis Santa Cruz GDAC" clean=1 mafToMatrix (inDir, outDir, cancer,flog, PATHPATTERN, suffix, namesuffix, dataProducer,REALRUN,clean, PLATFORM,distribution) clean=0 namesuffix = "mutation_ucsc" radia.radiaToXena (inDir, outDir, cancer,flog, PATHPATTERN, suffix, namesuffix, dataProducer,REALRUN,clean, PLATFORM,distribution)
def germline_ucsc_illuminaga_dnaseq_cont(inDir, outDir, cancer, flog, REALRUN): print cancer, sys._getframe().f_code.co_name distribution = False PATHPATTERN = "IlluminaGA_DNASeq_Cont." PLATFORM = "IlluminaGA" suffix = "ucsc" namesuffix = "germline_ucsc_vcf" dataProducer = "University of Californis Santa Cruz GDAC" clean = 0 type = "germline" radia.radiaToXena(inDir, outDir, cancer, flog, PATHPATTERN, suffix, namesuffix, dataProducer, REALRUN, clean, PLATFORM, distribution, type)
def ucsc_solid_dnaseq_cont(inDir, outDir, cancer, flog, REALRUN): print cancer, sys._getframe().f_code.co_name distribution = True PATHPATTERN = "SOLiD_DNASeq_Cont." PLATFORM = "SOLiD" suffix = "ucsc" namesuffix = "mutation_ucsc_solid_gene_maf" dataProducer = "University of Californis Santa Cruz GDAC" clean = 1 mafToMatrix(inDir, outDir, cancer, flog, PATHPATTERN, suffix, namesuffix, dataProducer, REALRUN, clean, PLATFORM, distribution) clean = 0 namesuffix = "mutation_ucsc" radia.radiaToXena(inDir, outDir, cancer, flog, PATHPATTERN, suffix, namesuffix, dataProducer, REALRUN, clean, PLATFORM, distribution)
def ucsc_illuminaga_dnaseq_cont_automated (inDir, outDir, cancer,flog,REALRUN): print cancer, sys._getframe().f_code.co_name distribution= False PATHPATTERN= "IlluminaGA_DNASeq_Cont_automated." PLATFORM = "IlluminaGA" suffix = "ucsc" namesuffix = "mutation_ucsc_maf_gene" dataProducer = "University of Californis Santa Cruz GDAC" clean=1 mafToMatrix (inDir, outDir, cancer,flog, PATHPATTERN, suffix, namesuffix, dataProducer,REALRUN,clean, PLATFORM,distribution) clean =0 namesuffix = "mutation_ucsc_maf" mafToXena (inDir, outDir, cancer,flog, PATHPATTERN, suffix, namesuffix, dataProducer,REALRUN,clean, PLATFORM,distribution) clean=0 namesuffix = "mutation_ucsc_vcf" type ="somatic" radia.radiaToXena (inDir, outDir, cancer,flog, PATHPATTERN, suffix, namesuffix, dataProducer,REALRUN,clean, PLATFORM,distribution,type)