directory = "/projects/dowellLab/ENCODE/HCT116"
bidirectionalfilepath = "/Users/joru1876/ENCODEBidirectional/bidirectional_hits.merge.shuffle.bed"
homedir = "/Users/joru1876/BidirectionalTFAnalyzer/src"
directorylist = fimo_directories(directory)
distances = dict()
for item in directorylist:
TF = item.split('/')[5]
distances[TF] = []
for item in directorylist:
print item
os.chdir(item)
TF = item.split('/')[5]
Motif = item.split('/')[8]
distances[TF].append(Motif)
distances[TF].append(Functions.get_distances_pad(bidirectionalfilepath, False, "fimo.rmdup.ord.cut.merge.bed", True, 1500))
os.chdir(homedir)
os.chdir('..')
os.chdir("files")
outfile = open("TFMotifToBidirDistancePadNegCntrl.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(",")
directory = "/Users/joru1876/HOCOMOCODatabaseFIMO/FIMO_OUT"
bidirectionalfilepath = "/Users/joru1876/ENCODEBidirectional/bidirectional_hits.merge.bed"
homedir = "/Users/joru1876/BidirectionalTFAnalyzer/src"
directorylist = ["/Users/joru1876/HOCOMOCODatabaseFIMO/FIMO_OUT/" + item for item in os.listdir(directory) if 'fimo_out' in item]
distances = dict()
for item in directorylist:
TF = item.split('/')[5].split('_')[0]
distances[TF] = []
for item in directorylist:
print item
os.chdir(item)
TF = item.split('/')[5].split('_')[0]
Functions.cut_file('fimo.txt', [1,2,3], Functions.get_mod_filename('fimo.txt', 'cut'))
distances[TF].append(Functions.get_distances_pad(bidirectionalfilepath, False, "fimo.cut.txt", True, 1500))
os.chdir(homedir)
os.chdir('..')
os.chdir("files")
outfile = open("TFMotifToBidirDistancePadDatabase.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(",")
