def run(directory):
directorylist = Functions.chip_peak_directories(directory)
for directory1 in directorylist:
os.chdir(directory1)
RemoveList = [item for item in os.listdir(directory1) if 'ENC' not in item and 'SL' not in item]
for item in RemoveList:
if '.' in item:
os.system("rm " + item)
else:
shutil.rmtree(directory1 + "/" + item)
def run(directory, maxsites, tomtomdir):
directorylist = Functions.chip_peak_directories(directory)
for item in directorylist:
if os.path.exists(item + "/outfiles"):
os.chdir(item + "/outfiles")
os.system("meme-chip ConsolidatedPeaks.merge.fasta -oc ./MEME meme-maxsites " + str(maxsites))
os.chdir(item + "/outfiles/MEME")
os.system("tomtom combined.meme " + tomtomdir)
else:
print "File not found in: " + item
def run(directory, referencefilepath):
directorylist = Functions.chip_peak_directories(directory)
for item in directorylist:
if os.path.exists(item + "/outfiles"):
os.chdir(item + "/outfiles")
os.system(
"bedtools getfasta -fi "
+ referencefilepath
+ " -bed ConsolidatedPeaks.merge.bed -fo ConsolidatedPeaks.merge.fasta"
)
else:
print "File not found in: " + item
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
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
if __name__ == "__main__":
directory = "/projects/dowellLab/ENCODE/HL60"
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 '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] + " > ConsolidatedPeaks.bed")
os.chdir("./outfiles")
os.system("bedtools merge -i ConsolidatedPeaks.bed > ConsolidatedPeaks.merge.bed")
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")
return BackgroundDict, FnoBDict, FandBDict
if __name__ == "__main__":
#Specify paths to directories or files
BidirFile = '/scratch/Users/joru1876/Allen2014_DMSO2_3-1_bidirectional_hits_intervals.bed'
ChipDir = '/scratch/Users/joru1876/HCT116v2'
FimoDir = '/scratch/Users/joru1876/HOCOMOCODatabaseFIMO'
FIMOTFDict = dict()
for TF in Functions.HOCOMOCO_fimo_directories(FimoDir):
TFlist = TF.split('/')
FIMOTFDict[TFlist[len(TFlist)-1][0:TFlist[len(TFlist)-1].index('_')]] = TF
ChipDirList = Functions.chip_peak_directories(ChipDir)
for directory in ChipDirList:
directorylist = directory.split('/')
TF = directorylist[len(directorylist)-2]
if TF in FIMOTFDict:
print TF
ChipFile = directory + '/' + [i for i in os.listdir(directory) if 'ENC' in i][0]
BackgroundDict, FnoBDict, FandBDict = run(BidirFile,ChipFile,FIMOTFDict[TF] + '/fimo.txt')
if not os.path.exists(Functions.parent_dir(directory) + '/ChIPPeakMotifValidator_out'):
os.mkdir(Functions.parent_dir(directory) + '/ChIPPeakMotifValidator_out')
os.chdir(Functions.parent_dir(directory) + '/ChIPPeakMotifValidator_out')
outfile1 = open('Background.txt','w')
for chrom in BackgroundDict:
outfile1.write(chrom)
outfile1.write('\t')
