Пример #1
0
def run():
    #Specify DMSO treated bedgraph directory
    DMSO = '/scratch/Users/joru1876/GROSeqRaw/flipped/bowtie2/sortedbam/genomecoveragebed/fortdf/JDR_DMSO_SS102217_093015_CAGATC_L005_R1_001.flip.fastqbowtie2.sorted.BedGraph.mp.BedGraph'

    #Specify CA treated bedgraph directory
    CA = '/scratch/Users/joru1876/GROSeqRaw/flipped/bowtie2/sortedbam/genomecoveragebed/fortdf/JDR_CA_SS102217_093015_ACTTGA_L005_R1_001.flip.fastqbowtie2.sorted.BedGraph.mp.BedGraph'

    #Specify gene annotations
    genes = '/scratch/Users/joru1876/GROSeqRaw/flipped/bowtie2/sortedbam/genomecoveragebed/fortdf/refGene.sorted.bed'

    #ChIP directory to get closest genes - currently set at SRF ChIP dataset
    chipdir = '/scratch/Shares/dowell/ENCODE/old/HCT116/SRF/peak_files/ENCFF001UEM.bed'

    #Specify list of genes to examine
    #genelist = ['CYR61','NR4A3','FOS','ATF3','EGR2','FOSB','JUN','NR4A1','DUSP1','NR4A2','DUSP2','EGR3','BTG2','WEE1','THBS1','ZFP36','SNF1LK','EGR1','JUNB','BHLHB2','AXUD1','PTG52','IER2','DUSP5','PLK2','GEM','GDF15','KLF6','SNORD102']

    #Home directory
    homedir = os.path.dirname(os.path.realpath(__file__))

    #File directory
    filedir = parent_dir(homedir) + '/files'

    #Figure directory
    figuredir = parent_dir(homedir) + '/figures'
    
    # print "Calculating closest genes to ChIP file..."
    # genelist = closest_gene.run(chipdir,genes,filedir)
    # genes = genelist
    print "Creating annotation files..."
    create_annotations.run(genes,filedir)
    TSS = filedir + '/TSS.sorted.bed'
    END = filedir + '/END.sorted.bed'
    print "done\nReflecting coverage values..."
    reflect_coverage.run(DMSO,CA,filedir)
    print "done\nCreating intersect files..."
    DMSOreflect = filedir + '/DMSO.bedgraph'
    CAreflect = filedir + '/CA.bedgraph'
    bedtools_create_intersects.run(DMSOreflect,CAreflect,genes,TSS,END,filedir)
    os.system("rm " + filedir + "/DMSO.bedgraph")
    os.system("rm " + filedir + "/CA.bedgraph")
    print "done\nGenerating files..."
    DMSOgenes = filedir + '/DMSO.genes.bed'
    DMSOTSS = filedir + '/DMSO.TSS.bed'
    DMSOEND = filedir + '/DMSO.END.bed'
    CAgenes = filedir + '/CA.genes.bed'
    CATSS = filedir + '/CA.TSS.bed'
    CAEND = filedir + '/CA.END.bed'
    master_writer.run(DMSOgenes,DMSOTSS,DMSOEND,CAgenes,CATSS,CAEND,filedir,figuredir)
    print "done"
    
    
Пример #2
0
if __name__ == "__main__":
    # Return parent directory
    def parent_dir(directory):
        pathlist = directory.split("/")
        newdir = "/".join(pathlist[0 : len(pathlist) - 1])

        return newdir

        # Home directory

    homedir = os.path.dirname(os.path.realpath(__file__))

    # File directory
    filedir = parent_dir(homedir) + "/files"

    # Figure directory
    figuredir = parent_dir(homedir) + "/figures"

    chipdir = "/scratch/Shares/dowell/ENCODE/old/HCT116/SRF/peak_files/ENCFF001UEM.bed"
    refseq = "/scratch/Users/joru1876/hg19_reference_files/refFlat_hg19.bed"
    # Specify DMSO treated bedgraph directory
    DMSO = "/scratch/Users/joru1876/GROSeqRaw/flipped/bowtie2/sortedbam/genomecoveragebed/fortdf/JDR_DMSO_SS102217_093015_CAGATC_L005_R1_001.flip.fastqbowtie2.sorted.BedGraph.mp.BedGraph"

    # Specify CA treated bedgraph directory
    CA = "/scratch/Users/joru1876/GROSeqRaw/flipped/bowtie2/sortedbam/genomecoveragebed/fortdf/JDR_CA_SS102217_093015_ACTTGA_L005_R1_001.flip.fastqbowtie2.sorted.BedGraph.mp.BedGraph"

    reflect_coverage.run(DMSO, CA, filedir)
    DMSOreflect = filedir + "/DMSO.bedgraph"
    CAreflect = filedir + "/CA.bedgraph"
    run(chipdir, refseq, filedir, DMSOreflect, CAreflect)