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"
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)