def ortholog(args):
"""
%prog ortholog species_a species_b
Run a sensitive pipeline to find orthologs between two species a and b.
The pipeline runs LAST and generate .lifted.anchors.
`--full` mode would assume 1-to-1 quota synteny blocks as the backbone of
such predictions. Extra orthologs will be recruited from reciprocal best
match (RBH).
"""
from jcvi.apps.last import main as last_main
from jcvi.compara.blastfilter import main as blastfilter_main
from jcvi.compara.quota import main as quota_main
from jcvi.compara.synteny import scan, mcscan, liftover
from jcvi.formats.blast import cscore, filter
p = OptionParser(ortholog.__doc__)
p.add_option("--full",
default=False,
action="store_true",
help="Run in full mode, including blocks and RBH")
p.add_option("--cscore",
default=0.7,
type="float",
help="C-score cutoff [default: %default]")
p.add_option("--dist",
default=20,
type="int",
help="Extent of flanking regions to search")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
a, b = args
abed, afasta = a + ".bed", a + ".cds"
bbed, bfasta = b + ".bed", b + ".cds"
ccscore = opts.cscore
dist = "--dist={0}".format(opts.dist)
aprefix = afasta.split(".")[0]
bprefix = bfasta.split(".")[0]
pprefix = ".".join((aprefix, bprefix))
qprefix = ".".join((bprefix, aprefix))
last = pprefix + ".last"
if need_update((afasta, bfasta), last):
last_main([bfasta, afasta, "-o", last])
if a == b:
last = filter([last, "--hitlen=0", "--pctid=98", "--inverse"])
filtered_last = last + ".filtered"
if need_update(last, filtered_last):
blastfilter_main([last, "--cscore={0}".format(ccscore)])
anchors = pprefix + ".anchors"
lifted_anchors = pprefix + ".lifted.anchors"
if not opts.full:
if need_update(filtered_last, lifted_anchors):
scan([filtered_last, anchors, dist, "--liftover={0}".format(last)])
return
if need_update(filtered_last, anchors):
scan([filtered_last, anchors, dist])
ooanchors = pprefix + ".1x1.anchors"
if need_update(anchors, ooanchors):
quota_main([anchors, "--quota=1:1", "--screen"])
lifted_anchors = pprefix + ".1x1.lifted.anchors"
if need_update((last, ooanchors), lifted_anchors):
liftover([last, ooanchors, dist])
pblocks = pprefix + ".1x1.blocks"
qblocks = qprefix + ".1x1.blocks"
if need_update(lifted_anchors, [pblocks, qblocks]):
mcscan([abed, lifted_anchors, "--iter=1", "-o", pblocks])
mcscan([bbed, lifted_anchors, "--iter=1", "-o", qblocks])
rbh = pprefix + ".rbh"
if need_update(last, rbh):
cscore([last, "-o", rbh])
portho = pprefix + ".ortholog"
qortho = qprefix + ".ortholog"
if need_update([pblocks, qblocks, rbh], [portho, qortho]):
make_ortholog(pblocks, rbh, portho)
make_ortholog(qblocks, rbh, qortho)
def ortholog(args):
"""
%prog ortholog species_a species_b
Run a sensitive pipeline to find orthologs between two species a and b.
The pipeline runs LAST and generate .lifted.anchors.
`--full` mode would assume 1-to-1 quota synteny blocks as the backbone of
such predictions. Extra orthologs will be recruited from reciprocal best
match (RBH).
"""
from jcvi.apps.last import main as last_main
from jcvi.compara.blastfilter import main as blastfilter_main
from jcvi.compara.quota import main as quota_main
from jcvi.compara.synteny import scan, mcscan, liftover
from jcvi.formats.blast import cscore, filter
p = OptionParser(ortholog.__doc__)
p.add_option("--full", default=False, action="store_true",
help="Run in full mode, including blocks and RBH")
p.add_option("--cscore", default=0.7, type="float",
help="C-score cutoff [default: %default]")
p.add_option("--dist", default=20, type="int",
help="Extent of flanking regions to search")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
a, b = args
abed, afasta = a + ".bed", a + ".cds"
bbed, bfasta = b + ".bed", b + ".cds"
ccscore = opts.cscore
dist = "--dist={0}".format(opts.dist)
aprefix = afasta.split(".")[0]
bprefix = bfasta.split(".")[0]
pprefix = ".".join((aprefix, bprefix))
qprefix = ".".join((bprefix, aprefix))
last = pprefix + ".last"
if need_update((afasta, bfasta), last):
last_main([bfasta, afasta, "-o", last])
if a == b:
last = filter([last, "--hitlen=0", "--pctid=98", "--inverse"])
filtered_last = last + ".filtered"
if need_update(last, filtered_last):
blastfilter_main([last, "--cscore={0}".format(ccscore)])
anchors = pprefix + ".anchors"
lifted_anchors = pprefix + ".lifted.anchors"
if not opts.full:
if need_update(filtered_last, lifted_anchors):
scan([filtered_last, anchors, dist,
"--liftover={0}".format(last)])
return
if need_update(filtered_last, anchors):
scan([filtered_last, anchors, dist])
ooanchors = pprefix + ".1x1.anchors"
if need_update(anchors, ooanchors):
quota_main([anchors, "--quota=1:1", "--screen"])
lifted_anchors = pprefix + ".1x1.lifted.anchors"
if need_update((last, ooanchors), lifted_anchors):
liftover([last, ooanchors, dist])
pblocks = pprefix + ".1x1.blocks"
qblocks = qprefix + ".1x1.blocks"
if need_update(lifted_anchors, [pblocks, qblocks]):
mcscan([abed, lifted_anchors, "--iter=1", "-o", pblocks])
mcscan([bbed, lifted_anchors, "--iter=1", "-o", qblocks])
rbh = pprefix + ".rbh"
if need_update(last, rbh):
cscore([last, "-o", rbh])
portho = pprefix + ".ortholog"
qortho = qprefix + ".ortholog"
if need_update([pblocks, qblocks, rbh], [portho, qortho]):
make_ortholog(pblocks, rbh, portho)
make_ortholog(qblocks, rbh, qortho)
def ortholog(args):
"""
%prog ortholog a.bed a.cds b.bed b.cds
Run a sensitive pipeline to find orthologs between two species a and b.
The pipeline runs LAST and 1-to-1 quota synteny blocks as the backbone of
such predictions. Extra orthologs will be recruited from reciprocal best
match (RBH).
"""
from jcvi.apps.last import main as last_main
from jcvi.compara.blastfilter import main as blastfilter_main
from jcvi.compara.quota import main as quota_main
from jcvi.compara.synteny import scan, mcscan, liftover
from jcvi.formats.blast import cscore
p = OptionParser(ortholog.__doc__)
p.add_option("--cscore", default=0.99, type="float", help="C-score cutoff [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
abed, afasta, bbed, bfasta = args
ccscore = opts.cscore
aprefix = afasta.split(".")[0]
bprefix = bfasta.split(".")[0]
pprefix = ".".join((aprefix, bprefix))
qprefix = ".".join((bprefix, aprefix))
last = pprefix + ".last"
if need_update((afasta, bfasta), last):
last_main([bfasta, afasta, "-o", last])
filtered_last = last + ".filtered"
bstring = ["--qbed=" + abed, "--sbed=" + bbed]
if need_update(last, filtered_last):
blastfilter_main([last, "--cscore={0}".format(ccscore), "--tandem_Nmax=10"] + bstring)
anchors = pprefix + ".anchors"
lifted_anchors = pprefix + ".lifted.anchors"
if need_update(filtered_last, lifted_anchors):
scan([filtered_last, anchors] + bstring)
ooanchors = pprefix + ".1x1.anchors"
if need_update(anchors, ooanchors):
quota_main([anchors, "--quota=1:1", "--screen"] + bstring)
lifted_anchors = pprefix + ".1x1.lifted.anchors"
if need_update((last, ooanchors), lifted_anchors):
liftover([last, ooanchors] + bstring)
pblocks = pprefix + ".1x1.blocks"
qblocks = qprefix + ".1x1.blocks"
if need_update(lifted_anchors, [pblocks, qblocks]):
mcscan([abed, lifted_anchors, "--iter=1", "-o", pblocks])
mcscan([bbed, lifted_anchors, "--iter=1", "-o", qblocks])
rbh = pprefix + ".rbh"
if need_update(last, rbh):
cscore([last, "-o", rbh])
portho = pprefix + ".ortholog"
qortho = qprefix + ".ortholog"
if need_update([pblocks, qblocks, rbh], [portho, qortho]):
make_ortholog(pblocks, rbh, portho)
make_ortholog(qblocks, rbh, qortho)