def last(args):
"""
%prog last old.fasta new.fasta
Generate psl file using last. Calles apps.last() but with special
parameters: -r5 -q95 -a0 -b95 -e500, which only reports alignments larger
than 100 bp and >=95 % identity.
"""
from jcvi.apps.last import main as lastapp
p = OptionParser(last.__doc__)
p.add_option("--distant",
default=False,
action="store_true",
help="Assume distant relations")
p.add_option(
"--minscore",
default=100,
type="int",
help="Filter alignments by how many bases match [default: %default]")
p.add_option("--minid",
default=95,
type="int",
help="Minimum sequence identity [default: %default]")
set_outfile(p)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
oldfasta, newfasta = args
args = [oldfasta, newfasta, "--format=maf", \
"--outfile={0}".format(opts.outfile)]
minscore = opts.minscore
minid = opts.minid
r = 100 - minid
q = minid
e = minscore * r
extra = r'--params=-r{0} -q{1} -a0 -b{1} -e{2}'.format(r, q, e)
if not opts.distant:
args.append(extra)
lastapp(args)
def last(args):
"""
%prog last old.fasta new.fasta
Generate psl file using LAST. Scoring parameters (-r -q -a -b -e)
automatically selected based on --minlen and --minid.
"""
from jcvi.apps.last import main as lastapp, supported_formats
p = OptionParser(last.__doc__)
p.add_option("--distant", default=False, action="store_true",
help="Assume distant relations")
p.add_option("--minlen", default=1000, type="int",
help="Filter alignments by how many bases match [default: %default]")
p.add_option("--minid", default=80, type="int",
help="Minimum sequence identity [default: %default]")
p.add_option("--format", default="maf", choices=supported_formats,
help="Output format")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
oldfasta, newfasta = args
args = [oldfasta, newfasta, "--format={0}".format(opts.format), \
"--outfile={0}".format(opts.outfile)]
minlen = opts.minlen
minid = opts.minid
assert minid != 100, "Perfect match not yet supported"
mm = minid / (100 - minid)
extra = r'--params=-r1 -q{0} -a{0} -b{0} -e{1}'.format(mm, minlen)
if not opts.distant:
args.append(extra)
lastapp(args)
def last(args):
"""
%prog last old.fasta new.fasta
Generate psl file using last. Calles apps.last() but with special
parameters: -r5 -q95 -a0 -b95 -e500, which only reports alignments larger
than 100 bp and >=95 % identity.
"""
from jcvi.apps.last import main as lastapp
p = OptionParser(last.__doc__)
p.add_option("--distant", default=False, action="store_true",
help="Assume distant relations")
p.add_option("--minscore", default=100, type="int",
help="Filter alignments by how many bases match [default: %default]")
p.add_option("--minid", default=95, type="int",
help="Minimum sequence identity [default: %default]")
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
oldfasta, newfasta = args
args = [oldfasta, newfasta, "--format=maf", \
"--outfile={0}".format(opts.outfile)]
minscore = opts.minscore
minid = opts.minid
r = 100 - minid
q = minid
e = minscore * r
extra = r'--params=-r{0} -q{1} -a0 -b{1} -e{2}'.format(r, q, e)
if not opts.distant:
args.append(extra)
lastapp(args)
