def replace_results(randoms_old, randoms_replace, directory, suffix,
replace_suffix, new_suffix):
rold = load_enhancers(randoms_old)
rreplace = load_enhancers(randoms_replace)
if rreplace == []:
return
e2 = rreplace.pop(0)
lines = []
for e in rold:
if e.id == e2.id:
lines.append(True)
if rreplace != []:
e2 = rreplace.pop(0)
else:
lines.append(False)
for filename in glob(directory + "/*" + suffix):
frep = open(filename + replace_suffix)
fnew = open(filename + new_suffix)
for i, line in enumerate(open(filename)):
if lines[i]:
fnew.write(frep.readline())
else:
fnew.write(line)
frep.close()
fnew.close()
def replace_randoms(randoms_old, randoms_replace, randoms_new):
rold = load_enhancers(randoms_old)
rreplace = load_enhancers(randoms_replace)
rnew = []
if rreplace == []:
return
e2 = rreplace.pop(0)
for e in rold:
if e.id == e2.id:
rnew.append(e2)
if rreplace != []:
e2 = rreplace.pop(0)
else:
rnew.append(e)
save_enhancers(rnew, randoms_new)
def replace_randoms(randoms_old, randoms_replace, randoms_new):
rold = load_enhancers(randoms_old)
rreplace = load_enhancers(randoms_replace)
rnew = []
if rreplace == []:
return
e2 = rreplace.pop(0)
for e in rold:
if e.id == e2.id:
rnew.append(e2)
if rreplace != []:
e2 = rreplace.pop(0)
else:
rnew.append(e)
save_enhancers(rnew, randoms_new)
def count_all_means(enhancers_file, directories, name):
enhancers = load_enhancers(enhancers_file)
print "nr of sequences:", len(enhancers)
names = [str(x.id) for x in enhancers]
try:
fails_file = open(DATAPATH + "%s.fails" % (name), "a")
except:
fails_file = open(DATAPATH + "%s.fails" % (name), "w+")
fails_file.write('\t'.join([' '] + names) + "\n")
print "saving fails number to %s%s.fails" % (DATAPATH, name)
n = len(names)
result = [0] * n
filenames = []
for directory in directories:
filenames += glob(directory + "/*.bigWig") + glob(directory + "/*.bw")
random.shuffle(filenames)
for filename in filenames:
fails = count_mean_signal(enhancers, filename, name)
if fails != []:
fails_file.write("\t".join([filename.split('/')[-1]] +
map(str, fails)) + "\n")
fails_file.close()
def count_all_means(enhancers_file, directories, name):
enhancers = load_enhancers(enhancers_file)
#print len(enhancers)
names = [str(x.id) for x in enhancers]
try:
fails_file = open(DATAPATH + "%s.fails" % (name), "a")
except:
fails_file = open(DATAPATH + "%s.fails" % (name), "w+")
fails_file.write('\t'.join([' '] + names) + "\n")
print "saving fails number to %s%s.fails" % (DATAPATH, name)
n = len(names)
result = [0] * n
filenames = []
for directory in directories:
filenames += glob(directory + "/*.bigWig") + glob(directory + "/*.bw")
pool = ThreadPool(N_pools)
fail_list = pool.map(lambda x: count_mean_signal(enhancers, x, name),
filenames)
pool.close()
for filename, fails in zip(filenames, fail_list):
if fails != []:
fails_file.write("\t".join([filename.split('/')[-1]] +
map(str, fails)) + "\n")
def replace_results(randoms_old, randoms_replace, directory, suffix, replace_suffix, new_suffix):
rold = load_enhancers(randoms_old)
rreplace = load_enhancers(randoms_replace)
if rreplace == []:
return
e2 = rreplace.pop(0)
lines = []
for e in rold:
if e.id == e2.id:
lines.append(True)
if rreplace != []:
e2 = rreplace.pop(0)
else:
lines.append(False)
for filename in glob(directory + "/*" + suffix):
frep = open(filename + replace_suffix)
fnew = open(filename + new_suffix)
for i, line in enumerate(open(filename)):
if lines[i]:
fnew.write(frep.readline())
else:
fnew.write(line)
frep.close()
fnew.close()
def change_random(randoms_file, to_remove):
enhancers = load_enhancers(randoms_file)
record_dict = SeqIO.index(home+"data/female.hg19.fa", "fasta")
to_return = []
for e in enhancers:
if e.id not in to_remove:
continue
while True:
l = e.end - e.start
start = random.randint(0,chr_lens[e.chromosome]-l-1)
if record_dict[e.chromosome].seq[start:(start+l)].find('N') == -1:
to_return.append(Position(e.chromosome, start, start + l, e.id, False, []))
break
else:
print e.chromosome
save_enhancers(to_return, randoms_file+".change")
return to_return
def change_random(randoms_file, to_remove):
enhancers = load_enhancers(randoms_file)
record_dict = SeqIO.index(home + "data/female.hg19.fa", "fasta")
to_return = []
for e in enhancers:
if e.id not in to_remove:
continue
while True:
l = e.end - e.start
start = random.randint(0, chr_lens[e.chromosome] - l - 1)
if record_dict[e.chromosome].seq[start:(start +
l)].find('N') == -1:
to_return.append(
Position(e.chromosome, start, start + l, e.id, False, []))
break
else:
print e.chromosome
save_enhancers(to_return, randoms_file + ".change")
return to_return
from ..shared import *
import load_vista
import sys
if __name__ == '__main__':
if len(sys.argv) < 4:
print "USAGE: add_sequences.py TYPE inputfile outputfile [start_id] [tissue]"
print "Genome file: %s%s, files_directory: %s" % (
DATAPATH, GENOME_FILE, DATAPATH)
sys.exit(1)
if len(sys.argv) == 6:
tissue = [sys.argv[5]]
positive = True
else:
tissue = []
positive = False
if sys.argv[1] == 'bed':
positions = load_vista.load_bed(sys.argv[2],
positive,
tissue,
startid=int(sys.argv[4]))
load_vista.add_seqs(positions, sys.argv[3])
else: #vista type
positions = load_vista.load_enhancers(sys.argv[2])
load_vista.add_seqs(positions, sys.argv[3])
x.end))
overlaps.append(x.id)
break
overlaps = list(set(overlaps))
return overlaps
if __name__ == "__main__":
dist = True
if len(sys.argv) < 4:
print "USAGE: overlaps.py from_file with_db tissue output"
print "output_directory: %s" % (DATAPATH)
sys.exit(1)
file1 = sys.argv[1]
db = sys.argv[2]
tissue = sys.argv[3]
outname = sys.argv[4]
remove = sorted(
check_overlap(load_enhancers(file1), load_target(db, tissue, False)))
print remove
with open(DATAPATH + outname, 'a+') as f:
#remove = [x for x in remove]
#print "removing %d"% len(set(remove))
f.write("\n".join([str(x) for x in remove]) + "\n")
f.close()
import sys
if __name__ =='__main__':
if len(sys.argv) < 4:
print "USAGE: add_sequences.py TYPE inputfile outputfile [start_id] [tissue]"
print "Genome file: %s%s, files_directory: %s"% (DATAPATH, GENOME_FILE, DATAPATH)
sys.exit(1)
if len(sys.argv) == 6:
tissue = [sys.argv[5]]
positive = True
else:
tissue = []
positive = False
if sys.argv[1] == 'bed':
positions = load_vista.load_bed(sys.argv[2], positive, tissue, startid=int(sys.argv[4]))
load_vista.add_seqs(positions, sys.argv[3])
else: #vista type
positions = load_vista.load_enhancers(sys.argv[2])
load_vista.add_seqs(positions, sys.argv[3])
overlaps=list(set(overlaps))
return overlaps
if __name__ == "__main__":
dist = True
if len(sys.argv) < 4:
print "USAGE: overlaps.py from_file with_db tissue output"
print "output_directory: %s"% ( DATAPATH)
sys.exit(1)
file1 = sys.argv[1]
db = sys.argv[2]
tissue = sys.argv[3]
outname = sys.argv[4]
remove = sorted(check_overlap(load_enhancers(file1), load_target(db, tissue, False)))
print remove
with open(DATAPATH+outname, 'a+') as f:
#remove = [x for x in remove]
#print "removing %d"% len(set(remove))
f.write("\n".join([str(x) for x in remove])+"\n")
f.close()