Python Functions.order_file 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: ChipRepConsolidator.py 프로젝트: jdrubin91/BidirectionalTFAnalyzer

def run(directory):
    directorylist = Functions.chip_peak_directories(directory)
    for item in directorylist:
        os.chdir(item)
        FileList = [file1 for file1 in os.listdir(item) if '.bed' in file1]
        if len(FileList) != 0:
            if 'outfiles' not in os.listdir(item):
                os.mkdir("./outfiles")
            if len(FileList) > 1:
                os.system("bedtools intersect -a " + FileList[0] + " -b " + " ".join(FileList[1:len(FileList)]) + " > ./outfiles/ConsolidatedPeaks.bed")
            else:
                os.system("cat " + FileList[0] + " > ./outfiles/ConsolidatedPeaks.bed")
            os.chdir("./outfiles")
            Functions.order_file("ConsolidatedPeaks.bed", "ConsolidatedPeaks.bed", False)
            os.system("bedtools merge -i ConsolidatedPeaks.bed > ConsolidatedPeaks.merge.bed")
        else:
            print "No bed files found in: " + item

예제 #3

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")