help="Save score histograms to FILE")
parser.add_argument('-j',
'--nthreads',
help="Number of threads.",
type=int,
default=16)
args = parser.parse_args()
if args.top:
import psutil
hra = HiriseAssembly()
hra.load_assembly(args.infile)
hra.merge_masked_regions(debug=args.debug)
print(len(hra.layout_lines))
if len(hra.layout_lines) == 0:
print("#make trivial layout")
hra.make_trivial_layout_lines(debug=args.debug)
ces.set_exp_insert_size_dist_fit_params(hra.model_params)
model = ces.model
nbams = len(hra.bams)
inq = JoinableQueue(maxsize=0)
readers = []
for i in range(nbams):
reader = Process(target=read_pairs_from_bam,
args=(inq, i, hra.bams[i], hra, args.mapq,
parser.add_argument(
"-o",
"--outfile",
default=False,
help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.",
)
# -m 2 -w 1000 -M $( cat {input.threshold} )
args = parser.parse_args()
if args.infile:
asf = HiriseAssembly()
asf.load_assembly(args.infile)
for segments_file in args.mask:
asf.add_mask_regions(filename=segments_file)
asf.merge_masked_regions()
if args.outfile:
of = open(args.outfile, "wt")
else:
of = sys.stdout
for ocontig in asf.ocontigs_iter():
chunk = struct.unpack("<L", hashlib.md5(ocontig.encode("utf-8")).digest()[:4])[0] % args.nchunks
if not chunk == args.chunk:
continue
links = {}
asf.get_links([ocontig], skipI=True, mapq=args.mapq, links=links, contigs=False, raw=True)
# print(ocontig,chunk,links)
process_links(links, args.window, args.min_links, args.max_others, segments=of)
of.close()
'-o',
'--outfile',
default=False,
help=
"Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking."
)
# -m 2 -w 1000 -M $( cat {input.threshold} )
args = parser.parse_args()
if args.infile:
asf = HiriseAssembly()
asf.load_assembly(args.infile)
for segments_file in args.mask:
asf.add_mask_regions(filename=segments_file)
asf.merge_masked_regions()
if args.outfile:
of = open(args.outfile, "wt")
else:
of = sys.stdout
for ocontig in asf.ocontigs_iter():
chunk = struct.unpack(
"<L",
hashlib.md5(
ocontig.encode("utf-8")).digest()[:4])[0] % args.nchunks
if not chunk == args.chunk: continue
links = {}
asf.get_links([ocontig],
skipI=True,
mapq=args.mapq,
parser.add_argument('-i','--infile',help="File containing .hra formatted hirise assembly.")
parser.add_argument('-o','--outfile',help="Output file name.")
parser.add_argument('-H','--histogram_file',help="Save score histograms to FILE")
parser.add_argument('-j','--nthreads',help="Number of threads.",type=int,default=16)
args = parser.parse_args()
if args.top:
import psutil
hra = HiriseAssembly()
hra.load_assembly(args.infile)
hra.merge_masked_regions(debug=args.debug)
print(len(hra.layout_lines))
if len(hra.layout_lines)==0:
print("#make trivial layout")
hra.make_trivial_layout_lines(debug=args.debug)
ces.set_exp_insert_size_dist_fit_params(hra.model_params)
model=ces.model
nbams = len(hra.bams)
inq = JoinableQueue(maxsize=0)
readers=[]
for i in range(nbams):
reader = Process(target=read_pairs_from_bam, args=(inq,i,hra.bams[i],hra,args.mapq,args.slice),daemon=False)
reader.start()
