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.align import last 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(
"--dbtype",
default="nucl",
choices=("nucl", "prot"),
help="Molecule type of subject database",
)
p.add_option(
"--full",
default=False,
action="store_true",
help="Run in full 1x1 mode, including blocks and RBH",
)
p.add_option("--cscore", default=0.7, type="float", help="C-score cutoff")
p.add_option(
"--dist", default=20, type="int", help="Extent of flanking regions to search"
)
p.add_option(
"-n",
"--min_size",
dest="n",
type="int",
default=4,
help="minimum number of anchors in a cluster",
)
p.add_option("--quota", help="Quota align parameter")
p.add_option(
"--no_strip_names",
default=False,
action="store_true",
help="Do not strip alternative splicing (e.g. At5g06540.1 -> At5g06540)",
)
p.set_cpus()
p.set_dotplot_opts()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
a, b = args
dbtype = opts.dbtype
suffix = ".cds" if dbtype == "nucl" else ".pep"
abed, afasta = a + ".bed", a + suffix
bbed, bfasta = b + ".bed", b + suffix
ccscore = opts.cscore
quota = opts.quota
dist = "--dist={0}".format(opts.dist)
minsize_flag = "--min_size={}".format(opts.n)
cpus_flag = "--cpus={}".format(opts.cpus)
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, cpus_flag], dbtype)
if a == b:
lastself = last + ".P98L0.inverse"
if need_update(last, lastself):
filter([last, "--hitlen=0", "--pctid=98", "--inverse", "--noself"])
last = lastself
filtered_last = last + ".filtered"
if need_update(last, filtered_last):
if opts.no_strip_names:
blastfilter_main([last, "--cscore={0}".format(ccscore), "--no_strip_names"])
else:
blastfilter_main([last, "--cscore={0}".format(ccscore)])
anchors = pprefix + ".anchors"
lifted_anchors = pprefix + ".lifted.anchors"
pdf = pprefix + ".pdf"
if not opts.full:
if need_update(filtered_last, lifted_anchors):
dargs = [
filtered_last,
anchors,
minsize_flag,
dist,
"--liftover={0}".format(last),
]
if opts.no_strip_names:
dargs += [
"--no_strip_names",
]
scan(dargs)
if quota:
quota_main([lifted_anchors, "--quota={0}".format(quota), "--screen"])
if need_update(anchors, pdf):
from jcvi.graphics.dotplot import dotplot_main
dargs = [anchors]
if opts.nostdpf:
dargs += ["--nostdpf"]
if opts.nochpf:
dargs += ["--nochpf"]
if opts.skipempty:
dargs += ["--skipempty"]
if opts.genomenames:
dargs += ["--genomenames", opts.genomenames]
if opts.theme:
dargs += ["--theme", opts.theme]
dotplot_main(dargs)
return
if need_update(filtered_last, anchors):
if opts.no_strip_names:
scan([filtered_last, anchors, dist, "--no_strip_names"])
else:
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):
if opts.no_strip_names:
liftover([last, ooanchors, dist, "--no_strip_names"])
else:
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 dotplot_main(args):
p = OptionParser(__doc__)
p.set_beds()
p.add_option(
"--synteny",
default=False,
action="store_true",
help="Run a fast synteny scan and display blocks",
)
p.add_option("--cmaptext",
help="Draw colormap box on the bottom-left corner")
p.add_option(
"--vmin",
dest="vmin",
type="float",
default=0,
help="Minimum value in the colormap",
)
p.add_option(
"--vmax",
dest="vmax",
type="float",
default=2,
help="Maximum value in the colormap",
)
p.add_option(
"--nmax",
dest="sample_number",
type="int",
default=10000,
help="Maximum number of data points to plot",
)
p.add_option(
"--minfont",
type="int",
default=4,
help="Do not render labels with size smaller than",
)
p.add_option("--colormap",
help="Two column file, block id to color mapping")
p.add_option(
"--nosort",
default=False,
action="store_true",
help="Do not sort the seqids along the axes",
)
p.add_option("--nosep",
default=False,
action="store_true",
help="Do not add contig lines")
p.add_option("--title", help="Title of the dot plot")
p.set_dotplot_opts()
p.set_outfile(outfile=None)
opts, args, iopts = p.set_image_options(args,
figsize="9x9",
style="dark",
dpi=90,
cmap="copper")
if len(args) != 1:
sys.exit(not p.print_help())
palette = opts.colormap
if palette:
palette = Palette(palette)
(anchorfile, ) = args
cmaptext = opts.cmaptext
if anchorfile.endswith(".ks"):
from jcvi.apps.ks import KsFile
logging.debug("Anchors contain Ks values")
cmaptext = cmaptext or "*Ks* values"
anchorksfile = anchorfile + ".anchors"
if need_update(anchorfile, anchorksfile):
ksfile = KsFile(anchorfile)
ksfile.print_to_anchors(anchorksfile)
anchorfile = anchorksfile
qbed, sbed, qorder, sorder, is_self = check_beds(anchorfile,
p,
opts,
sorted=(not opts.nosort))
if opts.skipempty:
ac = AnchorFile(anchorfile)
if is_self:
qseqids = sseqids = set()
else:
qseqids, sseqids = set(), set()
for pair in ac.iter_pairs():
q, s = pair[:2]
qi, q = qorder[q]
si, s = sorder[s]
qseqids.add(q.seqid)
sseqids.add(s.seqid)
if is_self:
qbed = sbed = subset_bed(qbed, qseqids)
else:
qbed = subset_bed(qbed, qseqids)
sbed = subset_bed(sbed, sseqids)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1]) # the whole canvas
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8]) # the dot plot
dotplot(
anchorfile,
qbed,
sbed,
fig,
root,
ax,
vmin=opts.vmin,
vmax=opts.vmax,
is_self=is_self,
synteny=opts.synteny,
cmap_text=opts.cmaptext,
cmap=iopts.cmap,
genomenames=opts.genomenames,
sample_number=opts.sample_number,
minfont=opts.minfont,
palette=palette,
sep=(not opts.nosep),
sepcolor=set1[int(opts.theme)],
title=opts.title,
stdpf=(not opts.nostdpf),
chpf=(not opts.nochpf),
)
image_name = opts.outfile or (op.splitext(anchorfile)[0] + "." +
opts.format)
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
fig.clear()