def main():
# Parse command line
options, args = doc_optparse.parse(__doc__)
try:
score_fname = args[0]
interval_fname = args[1]
if len(args) > 2:
out_file = open(args[2], 'w')
else:
out_file = sys.stdout
binned = bool(options.binned)
mask_fname = options.mask
except Exception:
doc_optparse.exit()
if binned:
scores_by_chrom = load_scores_ba_dir(score_fname)
else:
scores_by_chrom = load_scores_wiggle(score_fname)
if mask_fname:
masks = binned_bitsets_from_file(open(mask_fname))
else:
masks = None
for line in open(interval_fname):
fields = line.split()
chrom, start, stop = fields[0], int(fields[1]), int(fields[2])
total = 0
count = 0
min_score = 100000000
max_score = -100000000
for i in range(start, stop):
if chrom in scores_by_chrom and scores_by_chrom[chrom][i]:
# Skip if base is masked
if masks and chrom in masks:
if masks[chrom][i]:
continue
# Get the score, only count if not 'nan'
score = scores_by_chrom[chrom][i]
if not isNaN(score):
total += score
count += 1
max_score = max(score, max_score)
min_score = min(score, min_score)
if count > 0:
avg = total / count
else:
avg = "nan"
min_score = "nan"
max_score = "nan"
print("\t".join(
map(str, [chrom, start, stop, avg, min_score, max_score])),
file=out_file)
out_file.close()
def main():
# Parse command line
options, args = doc_optparse.parse(__doc__)
try:
score_fname = args[0]
interval_fname = args[1]
if len(args) > 2:
out_file = open(args[2], "w")
else:
out_file = sys.stdout
binned = bool(options.binned)
mask_fname = options.mask
except:
doc_optparse.exit()
if binned:
scores_by_chrom = load_scores_ba_dir(score_fname)
else:
scores_by_chrom = load_scores_wiggle(score_fname)
if mask_fname:
masks = binned_bitsets_from_file(open(mask_fname))
else:
masks = None
for line in open(interval_fname):
fields = line.split()
chrom, start, stop = fields[0], int(fields[1]), int(fields[2])
total = 0
count = 0
min_score = 100000000
max_score = -100000000
for i in range(start, stop):
if chrom in scores_by_chrom and scores_by_chrom[chrom][i]:
# Skip if base is masked
if masks and chrom in masks:
if masks[chrom][i]:
continue
# Get the score, only count if not 'nan'
score = scores_by_chrom[chrom][i]
if not isNaN(score):
total += score
count += 1
max_score = max(score, max_score)
min_score = min(score, min_score)
if count > 0:
avg = total / count
else:
avg = "nan"
min_score = "nan"
max_score = "nan"
print >> out_file, "\t".join(map(str, [chrom, start, stop, avg, min_score, max_score]))
out_file.close()
def __init__(self, wigFile):
'''read wig file, creat wig obj'''
self.scores = {}
self.num_re = re.compile(r'[\d\.\-\+]+')
fh = open(wigFile)
#infile=open(wigFile,'r')
for i, (chrom, pos, val) in enumerate(bx.wiggle.Reader(fh)):
chrom = chrom.upper()
if not chrom in self.scores: self.scores[chrom] = BinnedArray()
tmp = self.scores[chrom][pos]
if isNaN(tmp):
self.scores[chrom][pos] = val
else:
self.scores[chrom][pos] += val
if i % 100000 == 0: print "%i datapoints loaded \r" % i
#print self.scores.keys()
print "total " + str(i) + " points loaded"
def __init__(self,wigFile):
'''read wig file, creat wig obj'''
self.scores = {}
self.num_re=re.compile(r'[\d\.\-\+]+');
fh=open(wigFile)
#infile=open(wigFile,'r')
for i, ( chrom, pos, val ) in enumerate( bx.wiggle.Reader( fh ) ):
chrom=chrom.upper()
if not chrom in self.scores: self.scores[chrom] = BinnedArray()
tmp=self.scores[chrom][pos]
if isNaN(tmp):
self.scores[chrom][pos] = val
else:
self.scores[chrom][pos] += val
if i % 100000 == 0: print "%i datapoints loaded \r" % i
#print self.scores.keys()
print "total " + str(i) + " points loaded"
