def run(directory, bidirectionalfilepath, homedir):
fimodirectorylist = Functions.fimo_directories(directory)
counts = dict()
for fimo in fimodirectorylist:
TF = fimo.split('/')[5]
if TF not in counts:
counts[TF] = []
fimoname = fimo.split('/')[9]
fimofile = fimo + "/fimo.cut.rmdup.ord.merge.bed"
chipfile = Functions.parent_dir(Functions.parent_dir(fimo)) + '/ConsolidatedPeaks.merge.bed'
vennlist = Functions.venn_d3(bidirectionalfilepath, chipfile, fimofile)
counts[TF].append([fimoname, vennlist])
os.chdir(homedir)
os.chdir('..')
os.chdir("./files")
outfile = open("BidirChIpMotifOverlaps.txt",'w')
outfile.write("TF\nMotif#\nBidir\tChip\tMotif\tBC\tCB\tBM\tMB\tCM\tMC\tBCM\tCBM\tMBC\n")
for key in counts:
outfile.write(key)
outfile.write("\n")
for item in counts[key]:
outfile.write(item[0])
outfile.write("\n")
for value in item[1]:
outfile.write(value)
outfile.write("\t")
outfile.write("\n")
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")
def run(directory, bidirectionalfilepath, homedir):
directorylist = Functions.fimo_directories(directory)
def run(directory, bidirectionalfilepath, homedir):
TFdirectorylist = Functions.chip_peak_directories(directory)
fimodirectorylist = Functions.fimo_directories(directory)
counts = dict()
for item in TFdirectorylist:
if os.path.exists(item + "/outfiles"):
os.chdir(item + "/outfiles")
TF = item.split('/')[5]
counts[TF] = []
os.system("bedtools intersect -a " + bidirectionalfilepath + " -b ConsolidatedPeaks.merge.bed -c > Bidir_Chip_Counts.bed")
for item in fimodirectorylist:
os.chdir(item)
TF = item.split('/')[5]
fimo = item.split('/')[9]
os.system("bedtools intersect -a " + bidirectionalfilepath + " -b fimo.cut.rmdup.ord.merge.bed -c > Bidir_Motif_Counts.bed")
os.system("bedtools intersect -a " + directory + "/" + TF + "/peak_files/outfiles/ConsolidatedPeaks.merge.bed -b fimo.cut.rmdup.ord.merge.bed -c > Chip_Motif_Counts.bed")
BidirChipFile = open(directory + "/" + TF + "/peak_files/outfiles/Bidir_Chip_Counts.bed")
BidirMotifFile = open("Bidir_Motif_Counts.bed")
ChipMotifFile = open("Chip_Motif_Counts.bed")
BidirTot = Functions.line_count("Bidir_Motif_Counts.bed")
ChipTot = Functions.line_count("Chip_Motif_Counts.bed")
MotifTot = Functions.line_count("fimo.cut.rmdup.ord.merge.bed")
BidirChipCount = 0
ChipBidirCount = 0
BidirMotifCount = 0
MotifBidirCount = 0
ChipMotifCount = 0
MotifChipCount = 0
AllCount = 0
for line1 in BidirChipFile:
line2 = BidirMotifFile.readline()
x = int(line1.strip().split()[3])
y = int(line2.strip().split()[3])
if x != 0 and y != 0:
AllCount += 1.0
ChipBidirCount += x-1
MotifBidirCount += y-1
elif x != 0:
BidirChipCount += 1
ChipBidirCount += x
elif y != 0:
BidirMotifCount += 1
MotifBidirCount += y
for line3 in ChipMotifFile:
z = int(line3.strip().split()[3])
if z != 0:
ChipMotifCount += 1
MotifChipCount += z
ChipMotifCount = ChipMotifCount - AllCount
MotifChipCount = MotifChipCount - AllCount
BidirCount = BidirTot - AllCount - BidirChipCount - BidirMotifCount
ChipCount = ChipTot - AllCount - ChipMotifCount - ChipBidirCount
MotifCount = MotifTot - AllCount - MotifBidirCount - MotifChipCount
counts[TF].append([fimo, BidirCount, ChipCount, MotifCount, BidirChipCount, BidirMotifCount, ChipMotifCount, AllCount])
os.chdir(homedir)
os.chdir('..')
os.chdir("./files")
outfile = open("BidirChIpMotifOverlaps.txt",'w')
outfile.write("TF\nMotif#\nBidir\tChip\tMotif\tBC\tBM\tCM\tBCM\n")
for key in counts:
outfile.write(key)
outfile.write("\n")
for item in counts[key]:
outfile.write(item[0])
outfile.write("\n")
for i in range(1,len(item)):
outfile.write(str(item[i]))
outfile.write("\t")
outfile.write("\n")
