def tailblasr(query, target, nproc=1, outname="out.m5", basedir="./"):
"""
Try getting the read to hit each target uniquely instead of hoping that bestn reports all possible alignments
"""
global ALLTEMPFILES
#input reads
reads = FastqFile(query)
#map to make the primary
primary= NamedTemporaryFile(prefix="primary_", suffix=".m4", delete=False, dir=basedir)
primary = primary.name
ALLTEMPFILES.append(primary)
blasr(query, target, fmt="4", nproc=nproc, bestn=1, outname=primary)
#build command to call m4pie
args = "%s %s %s -t %d -n %d -o %s" % (primary, query, target, MINTAIL, nproc, outname)
args = args.split()
m4pie.run(args)
def tailblasr(query, target, nproc=1, outname="out.m5", basedir="./"):
"""
Try getting the read to hit each target uniquely instead of hoping that bestn reports all possible alignments
"""
global ALLTEMPFILES
#input reads
reads = FastqFile(query)
#map to make the primary
primary= NamedTemporaryFile(prefix="primary_", suffix=".m4", delete=False, dir=basedir)
primary = primary.name
ALLTEMPFILES.append(primary)
blasr(query, target, fmt="4", nproc=nproc, bestn=1, outname=primary)
#build command to call m4pie
args = "%s %s %s -t %d -n %d -o %s" % (primary, query, target, MINTAIL, nproc, outname)
args = args.split()
m4pie.run(args)