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")
__author__ = 'Jonathan Rubin'
import os
import sys
import Functions
if __name__ == "__main__":
file1 = sys.argv[1]
header1 = sys.argv[2]
file2 = sys.argv[3]
header2 = sys.argv[4]
file3 = sys.argv[5]
header3 = sys.argv[6]
if header1 == 'True':
header1 = True
if header2 == 'True':
header2 = True
if header3 == 'True':
header3 = True
print Functions.venn_d3(file1, header1, file2, header2, file3, header3)
return directorylist
directory = '/projects/dowellLab/ENCODE/HCT116'
bidirectionalfilepath = '/Users/joru1876/ENCODEBidirectional/bidirectional_hits.merge.bed'
homedir = '/Users/joru1876/test'
fimodirectorylist = fimo_directories(directory)
counts = dict()
for fimo in fimodirectorylist:
if os.path.exists(Functions.parent_dir(Functions.parent_dir(fimo)) + '/Consolidatedpeaks.ord.merge.bed'):
TF = fimo.split('/')[5]
if TF not in counts:
counts[TF] = []
fimoname = fimo.split('/')[8]
fimofile = fimo + "/fimo.rmdup.ord.cut.merge.bed"
chipfile = Functions.parent_dir(Functions.parent_dir(fimo)) + '/Consolidatedpeaks.ord.merge.bed'
vennlist = Functions.venn_d3(bidirectionalfilepath, False, chipfile, False, fimofile, True)
counts[TF].append([fimoname, vennlist])
os.chdir(homedir)
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(str(value))
outfile.write("\t")
outfile.write("\n")
