def main():
# Parse command line
options, args = doc_optparse.parse( __doc__ )
try:
if options.comp:
comp_type = options.comp
else:
comp_type = None
score_fname = args[0]
out_fname = args[1]
except:
doc_optparse.exit()
scores = BinnedArray()
## last_chrom = None
for i, ( chrom, pos, val ) in enumerate( bx.wiggle.Reader( misc.open_compressed( score_fname ) ) ):
#if last_chrom is None:
# last_chrom = chrom
#else:
# assert chrom == last_chrom, "This script expects a 'wiggle' input on only one chromosome"
scores[pos] = val
# Status
if i % 10000 == 0: print i, "scores processed"
out = open( out_fname, "w" )
if comp_type:
scores.to_file( out, comp_type=comp_type )
else:
scores.to_file( out )
out.close()
def main():
# Parse command line
options, args = doc_optparse.parse(__doc__)
try:
score_file = open(args[0])
interval_file = open(args[1])
if len(args) > 2:
out_file = open(args[2], 'w')
else:
out_file = sys.stdout
except:
doc_optparse.exit()
scores_by_chrom = read_scores(misc.open_compressed(sys.argv[1]))
for line in open(sys.argv[2]):
fields = line.split()
chrom, start, stop = fields[0], int(fields[1]), int(fields[2])
if chrom in scores_by_chrom:
ba = scores_by_chrom[chrom]
scores = [ba[i] for i in range(start, stop)]
else:
scores = []
print >> out_file, " ".join(fields), " ".join(map(str, scores))
score_file.close()
interval_file.close()
out_file.close()
def main():
# Parse command line
options, args = doc_optparse.parse(__doc__)
try:
score_file = open(args[0])
interval_file = open(args[1])
if len(args) > 2:
out_file = open(args[2], "w")
else:
out_file = sys.stdout
except:
doc_optparse.exit()
scores_by_chrom = read_scores(misc.open_compressed(sys.argv[1]))
for line in open(sys.argv[2]):
fields = line.split()
chrom, start, stop = fields[0], int(fields[1]), int(fields[2])
if chrom in scores_by_chrom:
ba = scores_by_chrom[chrom]
scores = [ba[i] for i in range(start, stop)]
else:
scores = []
print >> out_file, " ".join(fields), " ".join(map(str, scores))
score_file.close()
interval_file.close()
out_file.close()
def load_scores_wiggle(fname):
"""
Read a wiggle file and return a dict of BinnedArray objects keyed
by chromosome.
"""
scores_by_chrom = dict()
for chrom, pos, val in bx.wiggle.Reader(misc.open_compressed(fname)):
if chrom not in scores_by_chrom:
scores_by_chrom[chrom] = BinnedArray()
scores_by_chrom[chrom][pos] = val
return scores_by_chrom
def load_scores_wiggle( fname ):
"""
Read a wiggle file and return a dict of BinnedArray objects keyed
by chromosome.
"""
scores_by_chrom = dict()
for chrom, pos, val in bx.wiggle.Reader( misc.open_compressed( fname ) ):
if chrom not in scores_by_chrom:
scores_by_chrom[chrom] = BinnedArray()
scores_by_chrom[chrom][pos] = val
return scores_by_chrom
def main():
intersecters = {}
# Read ranges
for chr, start, end in read_intervals( misc.open_compressed( sys.argv[1] ) ):
if not intersecters.has_key( chr ): intersecters[ chr ] = intervals.Intersecter()
intersecters[ chr ].add_interval( intervals.Interval( start, end ) )
# Count intersection
total = 0
for chr, start, end in read_intervals( misc.open_compressed( sys.argv[2] ) ):
if intersecters.has_key( chr ):
intersection = intersecters[ chr ].find( start, end )
if intersection:
#print chr, intersection
total += 1
print total
def main():
intersecters = {}
# Read ranges
for chr, start, end in read_intervals( misc.open_compressed( sys.argv[1] ) ):
if not intersecters.has_key( chr ): intersecters[ chr ] = intervals.Intersecter()
intersecters[ chr ].add_interval( intervals.Interval( start, end ) )
# Count intersection
total = 0
for chr, start, end in read_intervals( misc.open_compressed( sys.argv[2] ) ):
if intersecters.has_key( chr ):
intersection = intersecters[ chr ].find( start, end )
if intersection:
#print chr, intersection
total += 1
print total