def BinsFromBigWig(bwfile,binsize):
''' Read bins from BigWig file.'''
Bins={}
chroms=Utils.getBigWigChroms(bwfile)
for chrom in chroms:
Bins[chrom]=numpy.zeros(chroms[chrom]/binsize)
for start,stop,val in IO.BigWigReader(bwfile,chrom):
Bins[chrom][start/binsize]=val
return Bins
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
# Get parameters
args = argParser()
# genome={}
# for line in IO.ColumnReader(args.genome):
# genome[line[0]]=int(line[1])
genome = Utils.genomeSize(args.genome)
counts = {}
gsize = float(sum(genome.values()))
# number of Beds in each chrom
for chrom in genome:
counts[chrom] = int(genome[chrom] / gsize * args.number + 0.5)
# check number
diff = sum(counts.values()) - args.number
chroms = counts.keys()
chroms.sort()
if diff != 0:
for i in diff > 0 and range(diff) or range(diff, 0):
j = randint(1, len(counts))
counts[chroms[j - 1]] += diff > 0 and -1 or 1
# generate Beds
cnt = 1