Python radiaToXena Exemples

Exemple #1

Fichier : maf.py Projet : jianguozhouzunyimedicaluniversity/wrangle

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)

Exemple #2

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)

Exemple #3

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)

Exemple #4

Fichier : maf.py Projet : jianguozhouzunyimedicaluniversity/wrangle

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)

Exemple #5

Fichier : maf.py Projet : jianguozhouzunyimedicaluniversity/wrangle

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)

Exemple #6

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)