def run(directory): directorylist = Functions.fimo_directories(directory) for item in directorylist: os.chdir(item) FileList = Functions.parse_file("fimo.txt") Functions.cut_file("fimo.txt", [i for i in range(1, len(FileList[0]))], "fimo.cut.bed") Functions.remove_duplicates_int("fimo.cut.bed", "fimo.cut.rmdup.bed", True) Functions.order_file("fimo.cut.rmdup.bed", "fimo.cut.rmdup.ord.bed", True) Functions.replace_header("fimo.cut.rmdup.ord.bed", "#chrom\tstart\tstop\tstrand") os.system("bedtools merge -i fimo.cut.rmdup.ord.bed > fimo.cut.rmdup.ord.merge.bed")
import os import Functions ##Removes duplicates and creates non-overlapping intervals for FIMO files def run(directory): directorylist = Functions.fimo_directories(directory) for item in directorylist: os.chdir(item) FileList = Functions.parse_file("fimo.txt") Functions.cut_file("fimo.txt", [i for i in range(1, len(FileList[0]))], "fimo.cut.bed") Functions.remove_duplicates_int("fimo.cut.bed", "fimo.cut.rmdup.bed", True) Functions.order_file("fimo.cut.rmdup.bed", "fimo.cut.rmdup.ord.bed", True) Functions.replace_header("fimo.cut.rmdup.ord.bed", "#chrom\tstart\tstop\tstrand") os.system("bedtools merge -i fimo.cut.rmdup.ord.bed > fimo.cut.rmdup.ord.merge.bed") if __name__ == "__main__": directory = "/projects/dowellLab/ENCODE/HL60" directorylist = Functions.fimo_directories(directory) for item in directorylist: os.chdir(item) FileList = Functions.parse_file("fimo.txt") Functions.cut_file("fimo.txt", [i for i in range(1, len(FileList[0]))], "fimo.cut.bed") Functions.remove_duplicates_int("fimo.cut.bed", "fimo.cut.rmdup.bed", True) Functions.order_file("fimo.cut.rmdup.bed", "fimo.cut.rmdup.ord.bed", True) Functions.replace_header("fimo.cut.rmdup.ord.bed", "#chrom\tstart\tstop\tstrand") os.system("bedtools merge -i fimo.cut.rmdup.ord.bed > fimo.cut.rmdup.ord.merge.bed")