Python Functions.remove_duplicates_int 예제들

예제 #1

파일: FimoFix.py 프로젝트: jdrubin91/BidirectionalTFAnalyzer

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")

예제 #2

파일: FimoFix.py 프로젝트: jdrubin91/BidirectionalTFAnalyzer

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")