def Main():
args=ArgParse()
# initiate genome object from UCSC genome browser
chromInfo=Genome(db=args.genome).chromInfo
chroms={}
sum_size=0
sum_size_list=[]
#store chromInfo
for i in range(chromInfo.count()):
try:
if "random" in chromInfo[i].chrom: continue
chroms[chromInfo[i].chrom]=chromInfo[i].size
sum_size+=chromInfo[i].size
sum_size_list.append((chromInfo[i].chrom,sum_size))
except:
break
print >> sys.stderr, sum_size_list[-1][1]
print >> sys.stderr, chroms
print >>sys.stderr, "Chromosome information readed, %d chromosomes"%(len(chroms))
i=0
while i < args.num:
# randomly select one chromosome and a region in this chromosome
chrom=random_chr(sum_size_list)
size=chroms[chrom]
length=int(gauss(args.mean,args.sd))
start=randrange(1,size-length-1)
end=start+length-1
strand=choice(['+','-'])
print "\t".join(str(f) for f in [chrom,start,end,i+1,0,strand])
i=i+1
def Main():
args = ArgParse()
# initiate genome object from UCSC genome browser
chromInfo = Genome(db=args.genome).chromInfo
chroms = {}
sum_size = 0
sum_size_list = []
#store chromInfo
for i in range(chromInfo.count()):
try:
if "random" in chromInfo[i].chrom: continue
chroms[chromInfo[i].chrom] = chromInfo[i].size
sum_size += chromInfo[i].size
sum_size_list.append((chromInfo[i].chrom, sum_size))
except:
break
print >> sys.stderr, sum_size_list[-1][1]
print >> sys.stderr, chroms
print >> sys.stderr, "Chromosome information readed, %d chromosomes" % (
len(chroms))
i = 0
while i < args.num:
# randomly select one chromosome and a region in this chromosome
chrom = random_chr(sum_size_list)
size = chroms[chrom]
length = int(gauss(args.mean, args.sd))
start = randrange(1, size - length - 1)
end = start + length - 1
strand = choice(['+', '-'])
print "\t".join(str(f) for f in [chrom, start, end, i + 1, 0, strand])
i = i + 1
