last_x=0
contign=0
contig,p=end[:-2],end[-1:]
if not contig in scaffold_hash:
print("scaffold:",contig,scaffold)
scaffold_hash[contig]=scaffold
if (not contig == last_c) and last_s==scaffold:
if not (contig,last_c) in bl:
print("\t".join(map(str,["#edge:",last_end,end,{'length':int(x-last_x),'contig':False}])))
elif last_c==contig:
if args.breaks and is_broken(contig,breaks):
new_scaffold = scaffold_raw + idGen.id()
scaffold_rename[scaffold_raw]=new_scaffold
if p=="3" : ## contig on the + strand
#
# new_3prime_end = end
print("\t".join(map(str,["#edge:",last_end,end,{'length':int(x-last_x),'contig':True}])))
print("\t".join(map(str,["#edge:",last_end,end,{'length':int(x-last_x),'contig':True}])))
end = new_contig + ".3"
contig = new_contig
scaffold= new_scaffold
else: ## contig on the - strand
scaffold_hash[contig] = scaffold
if (not contig == last_c) and last_s == scaffold:
if not (contig, last_c) in bl:
print("\t".join(
map(str, [
"#edge:", last_end, end, {
'length': int(x - last_x),
'contig': False
}
])))
elif last_c == contig:
if args.breaks and is_broken(contig, breaks):
new_scaffold = scaffold_raw + idGen.id()
scaffold_rename[scaffold_raw] = new_scaffold
if p == "3": ## contig on the + strand
#
# new_3prime_end = end
print("\t".join(
map(str, [
"#edge:", last_end, end, {
'length': int(x - last_x),
'contig': True
}
])))
print("\t".join(
map(str, [
pysam.faidx(args.fasta)
fastafile = pysam.Fastafile(args.fasta)
outfasta = fastaWriter(args.outfile)
# print("opened outfile", file=sys.stderr)
logfile = False
if args.logfile: logfile = open(args.logfile, "wt")
name_prefix = ""
if args.prefix:
name_prefix = args.prefix
else:
import idGen as idGen
name_prefix = "Sc" + idGen.id()
print("name_prefix", name_prefix, file=sys.stderr)
# for i in range(5):
# name_prefix += random.choice( "123456789ABCDEFGHJKLMNPQRSTUVWXYZabcdefghijkmnopqrstuvwxyz" )
#31 Scaffold142609_1.5 GGGGTACCAGGTGTCTGGGTGCTGGCAGAGCCGGCACTGATGTTTTCTGGG Scaffold41854_1.5 GGTACCAGGTGTCTGGGTGCTGGCAGAGCCGGCACTGATGTTTTCTGGGGG GGGGTACCAGGTGTCTGGGTGCTGGCAGAGCCGGCACTGATGTTTTCTGGGGG
gapclose_data = {}
if args.gapclose:
fh = open(args.gapclose)
while True:
l = fh.readline()
if not l: break
if l[0] == "#": continue
scaffold, end1, kmer1, end2, kmer2, closure = l.strip().split()
gapclose_data[end1, end2] = (kmer1, kmer2, closure)
pysam.faidx(args.fasta)
fastafile = pysam.Fastafile( args.fasta )
outfasta=fastaWriter(args.outfile)
# print("opened outfile", file=sys.stderr)
logfile=False
if args.logfile: logfile=open(args.logfile,"wt")
name_prefix=""
if args.prefix:
name_prefix=args.prefix
else:
import idGen as idGen
name_prefix="Sc" + idGen.id()
print("name_prefix",name_prefix,file=sys.stderr)
# for i in range(5):
# name_prefix += random.choice( "123456789ABCDEFGHJKLMNPQRSTUVWXYZabcdefghijkmnopqrstuvwxyz" )
#31 Scaffold142609_1.5 GGGGTACCAGGTGTCTGGGTGCTGGCAGAGCCGGCACTGATGTTTTCTGGG Scaffold41854_1.5 GGTACCAGGTGTCTGGGTGCTGGCAGAGCCGGCACTGATGTTTTCTGGGGG GGGGTACCAGGTGTCTGGGTGCTGGCAGAGCCGGCACTGATGTTTTCTGGGGG
gapclose_data={}
if args.gapclose:
fh=open(args.gapclose)
while True:
l=fh.readline()
if not l: break
if l[0]=="#": continue
scaffold,end1,kmer1,end2,kmer2,closure=l.strip().split()
gapclose_data[end1,end2]=(kmer1,kmer2,closure)
#!/usr/bin/env python3
import idGen
id = idGen.id()
print("\nYour generated ID is:\n{}".format(id))
