def jd2washU(fs, fout, cut, ext):
"""
Convert PETs to washU long range interactions.
Track format according to http://wiki.wubrowse.org/Long-range
@param fs: files of .jd files
@param fout: prefix of output files
"""
print "Converting %s to washU track." % (",".join(fs))
tmp = str(random.random())
with open(tmp, "w") as f:
for fin in fs:
print "converting %s" % fin
key, mat = parseJd(fin, cut)
for t in mat:
a = (key[0], max([0, t[1] - ext]), t[1] + ext)
b = (key[1], max([0, t[2] - ext]), t[2] + ext)
linea = [
a[0], a[1], a[2],
"%s:%s-%s,1" % (b[0], b[1], b[2]), t[0], "."
]
lineb = [
b[0], b[1], b[2],
"%s:%s-%s,1" % (a[0], a[1], a[2]), t[0], "."
]
f.write("\t".join(map(str, linea)) + "\n")
f.write("\t".join(map(str, lineb)) + "\n")
c1 = "bedtools sort -i %s > %s" % (tmp, fout)
c2 = "rm %s" % tmp
c3 = "bgzip %s" % fout
c4 = "tabix -p bed %s.gz" % fout
callSys([c1, c2, c3, c4])
print "Converting %s to washU random accessed track finished." % fout
def loops2washU(fin, fout, logger, significant=1):
"""
Convert interaction level loop file to washU long range interactions.
Track format according to http://wiki.wubrowse.org/Long-range
@param fin: interactions in loop file
@param fout: washU long-range interaction text file prefix
@param significant: if set 1, only convert significant loops.
"""
logger.info("Converting %s to washU long range interaction track." % fin)
tmp = str(random.random())
with open(tmp, "w") as f:
for i, line in enumerate(open(fin)):
if i == 0:
continue
line = line.split("\n")[0].split("\t")
#only using significant results
if significant and float(line[-1]) < 1:
continue
if str(line[1]) == "inf":
line[1] = 100
a = parseIv(line[6])
b = parseIv(line[7])
linea = [
a[0], a[1], a[2],
"%s,1" % line[7]
]
lineb = [
b[0], b[1], b[2],
"%s,1" % line[6]
]
f.write("\t".join(map(str, linea)) + "\n")
f.write("\t".join(map(str, lineb)) + "\n")
c1 = "bedtools sort -i %s > %s" % (tmp, fout)
c2 = "rm %s" % tmp
c3 = "bgzip %s" % fout
c4 = "tabix -p bed %s.gz" % fout
callSys([c1, c2, c3, c4])
logger.info(
"Converting %s to washU long range interaction track finished." % fin)
def jd2hic(fs, fout, cut, org, resolution):
"""
Convert reads level bedpe to HIC.
Track format according to https://github.com/theaidenlab/juicer/wiki/Pre#file-format
@param fs: files of .jd files
@param fout: prefix of output files
"""
print "Converting %s to .hic file which could be loaded in juicebox" % (
",".join(fs))
tmp = str(random.random())
ss = {"+": 0, "-": 1}
with open(tmp, "w") as f:
for fin in fs:
print "converting %s" % fin
key, mat = parseJd(fin, cut)
for t in mat:
line = [0, key[0], t[1], 0, 1, key[1], t[2], 1]
f.write("\t".join(map(str, line)) + "\n")
c1 = "juicer_tools pre -n -r {resolution} -d {fin} {fout} {org}".format(
resolution=resolution, fin=tmp, fout=fout, org=org)
c2 = "rm %s" % tmp
callSys([c1, c2])
print "Converting %s to juicer's hic file finished." % fout