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")
file1 = open(filename1)
motiflist = []
for line1 in file1:
if 'MOTIF' in line1:
motif = line1.strip().split()[1]
motiflist.append(motif)
return motiflist
if __name__ == "__main__":
#Right now this calls fimo on each motif by providing the HOCOMOCO database along with a single motif name per
#job submitted. It now only submits jobs for motifs who have fimo.txt files less than 1
shellscripttemplatedir = '/Users/joru1876/HOCOMOCODatabaseFIMO'
packagedir = '/Users/joru1876/BidirectionalTFAnalyzer'
motiflist = run(packagedir + '/files/HOCOMOCOv9_AD_MEME.txt', True)
motiflist1 = []
for item in motiflist:
if not os.path.exists(shellscripttemplatedir + "/FIMO_OUT/" + item +"_fimo_out"+ "/fimo.txt") or Functions.line_count(shellscripttemplatedir + "/FIMO_OUT/" + item +"_fimo_out"+ "/fimo.txt") < 2:
motiflist1.append(item)
print motiflist1
print len(motiflist1)
os.chdir(shellscripttemplatedir)
for motif in motiflist1:
os.system("qsub -v arg1='/Users/joru1876/HOCOMOCODatabaseFIMO/FIMO_OUT/" + motif + "_fimo_out',arg2='" + motif + "' runHOCOMOCOv9FIMOTemplate.sh")
TF = item.split('/')[5]
counts[TF] = []
os.system("bedtools intersect -a " + bidirectionalfilepath + " -b Consolidatedpeaks.ord.merge.bed -c > Bidir_Chip_Counts.bed")
for item in fimodirectorylist:
os.chdir(item)
TF = item.split('/')[5]
print TF
fimo = item.split('/')[8]
os.system("bedtools intersect -a " + bidirectionalfilepath + " -b fimo.rmdup.ord.cut.merge.bed -c > Bidir_Motif_Counts.bed")
os.system("bedtools intersect -a " + directory + "/" + TF + "/peak_files/Consolidatedpeaks.ord.merge.bed -b fimo.rmdup.ord.cut.merge.bed -c > Chip_Motif_Counts.bed")
BidirChipFile = open(directory + "/" + TF + "/peak_files/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.rmdup.ord.cut.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
