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")
def run(directory, bidirectionalfilepath, homedir):
directorylist = Functions.fimo_directories(directory)
distances = dict()
for item in directorylist:
if os.path.exists(item):
os.chdir(item)
TF = item.split('/')[5]
Motif = item.split('/')[9]
os.system("bedtools intersect -a " + bidirectionalfilepath + " -b fimo.cut.rmdup.ord.merge.bed -wa -wb > BidirectionalMotifIntersect.bed")
FileList = Functions.parse_file("BidirectionalMotifIntersect.bed")
fimodist = []
for line in FileList:
chrom1, start1, stop1, chrom2, start2, stop2 = line[0:6]
i = (float(start1) + float(stop1))/2
x = (float(start2) + float(stop2))/2
fimodist.append((i-x)/(float(stop1)-float(start1)))
if len(fimodist) > 0:
if TF in distances:
distances[TF].append(Motif)
distances[TF].append(fimodist)
else:
distances[TF] = [Motif, fimodist]
os.chdir(homedir)
os.chdir('..')
os.chdir("./files")
outfile = open("TFMotifToBidirDistance.txt",'w')
for key in distances:
outfile.write(key)
outfile.write("\n")
for item in distances[key]:
if 'fimo_out' in item:
outfile.write(str(item))
else:
for value in item:
outfile.write(str(value))
outfile.write(",")
outfile.write("\n")
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")
for fimofolder in FileList:
directorylist.append(rootdirectory + "/" + TF + "/peak_files/MEME/" + fimofolder)
return directorylist
directory = "/projects/dowellLab/ENCODE/HCT116"
bidirectionalfilepath = "/Users/joru1876/ENCODEBidirectional/bidirectional_hits.merge.bed"
homedir = "/Users/joru1876/BidirectionalTFAnalyzer/src"
directorylist = fimo_directories(directory)
distances = dict()
for item in directorylist:
os.chdir(item)
TF = item.split('/')[5]
Motif = item.split('/')[8]
os.system("bedtools intersect -a " + bidirectionalfilepath + " -b fimo.rmdup.ord.cut.merge.bed -wa -wb > BidirectionalMotifIntersect.bed")
FileList = Functions.parse_file("BidirectionalMotifIntersect.bed")
fimodist = []
for line in FileList:
chrom1, start1, stop1, chrom2, start2, stop2 = line[0:6]
i = (float(start1) + float(stop1))/2
x = (float(start2) + float(stop2))/2
fimodist.append((i-x)/((float(stop1)-float(start1))/2))
if len(fimodist) > 0:
if TF in distances:
samplemean = np.mean(fimodist)
samplestanddev = np.std(fimodist)
z = samplemean/(samplestanddev/math.sqrt(len(fimodist)))
distances[TF].append(Motif)
distances[TF].append(fimodist)
else:
distances[TF] = [Motif, fimodist]
def run(fimodir):
fimofile = fimodir + "/fimo.txt"
return Functions.parse_file(fimodir + "/fimo.txt")[1 : len(Functions.parse_file(fimodir + "/fimo.txt"))]
