def plotall(xargs):
"""
%prog plotall input.bed
Plot the matchings between the reconstructed pseudomolecules and the maps.
This command will plot each reconstructed object (non-singleton).
"""
p = OptionParser(plotall.__doc__)
add_allmaps_plot_options(p)
opts, args, iopts = p.set_image_options(xargs, figsize="10x6")
if len(args) != 1:
sys.exit(not p.print_help())
inputbed, = args
pf = inputbed.rsplit(".", 1)[0]
agpfile = pf + ".agp"
agp = AGP(agpfile)
objects = [ob for ob, lines in agp.iter_object() if len(lines) > 1]
for seqid in sorted(objects):
plot(xargs + [seqid])
def plotall(xargs):
"""
%prog plotall input.bed
Plot the matchings between the reconstructed pseudomolecules and the maps.
This command will plot each reconstructed object (non-singleton).
"""
p = OptionParser(plotall.__doc__)
add_allmaps_plot_options(p)
opts, args, iopts = p.set_image_options(xargs, figsize="10x6")
if len(args) != 1:
sys.exit(not p.print_help())
inputbed, = args
pf = inputbed.rsplit(".", 1)[0]
agpfile = pf + ".agp"
agp = AGP(agpfile)
objects = [ob for ob, lines in agp.iter_object() if len(lines) > 1]
for seqid in sorted(objects):
plot(xargs + [seqid])
def estimategaps(args):
"""
%prog estimategaps input.bed
Estimate sizes of inter-scaffold gaps. The AGP file generated by path()
command has unknown gap sizes with a generic number of Ns (often 100 Ns).
The AGP file `input.chr.agp` will be modified in-place.
"""
p = OptionParser(estimategaps.__doc__)
p.add_option("--minsize", default=100, type="int", help="Minimum gap size")
p.add_option("--maxsize",
default=500000,
type="int",
help="Maximum gap size")
p.add_option("--links",
default=10,
type="int",
help="Only use linkage grounds with matchings more than")
p.set_verbose(help="Print details for each gap calculation")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
inputbed, = args
pf = inputbed.rsplit(".", 1)[0]
agpfile = pf + ".chr.agp"
bedfile = pf + ".lifted.bed"
cc = Map(bedfile, scaffold_info=True)
agp = AGP(agpfile)
minsize, maxsize = opts.minsize, opts.maxsize
links = opts.links
verbose = opts.verbose
outagpfile = pf + ".estimategaps.agp"
fw = must_open(outagpfile, "w")
for ob, components in agp.iter_object():
components = list(components)
s = Scaffold(ob, cc)
mlg_counts = s.mlg_counts
gaps = [x for x in components if x.is_gap]
gapsizes = [None] * len(gaps) # master
for mlg, count in mlg_counts.items():
if count < links:
continue
g = GapEstimator(cc, agp, ob, mlg)
g.compute_all_gaps(minsize=minsize, maxsize=maxsize, \
verbose=verbose)
# Merge evidence from this mlg into master
assert len(g.gapsizes) == len(gaps)
for i, gs in enumerate(gapsizes):
gg = g.gapsizes[i]
if gs is None:
gapsizes[i] = gg
elif gg:
gapsizes[i] = min(gs, gg)
print gapsizes
# Modify AGP
i = 0
for x in components:
if x.is_gap:
x.gap_length = gapsizes[i] or minsize
x.component_type = 'U' if x.gap_length == 100 else 'N'
i += 1
print >> fw, x
fw.close()
reindex([outagpfile, "--inplace"])
def estimategaps(args):
"""
%prog estimategaps input.bed
Estimate sizes of inter-scaffold gaps. The AGP file generated by path()
command has unknown gap sizes with a generic number of Ns (often 100 Ns).
The AGP file `input.chr.agp` will be modified in-place.
"""
p = OptionParser(estimategaps.__doc__)
p.add_option("--minsize", default=100, type="int",
help="Minimum gap size")
p.add_option("--maxsize", default=500000, type="int",
help="Maximum gap size")
p.add_option("--links", default=10, type="int",
help="Only use linkage grounds with matchings more than")
p.set_verbose(help="Print details for each gap calculation")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
inputbed, = args
pf = inputbed.rsplit(".", 1)[0]
agpfile = pf + ".chr.agp"
bedfile = pf + ".lifted.bed"
cc = Map(bedfile, scaffold_info=True)
agp = AGP(agpfile)
minsize, maxsize = opts.minsize, opts.maxsize
links = opts.links
verbose = opts.verbose
outagpfile = pf + ".estimategaps.agp"
fw = must_open(outagpfile, "w")
for ob, components in agp.iter_object():
components = list(components)
s = Scaffold(ob, cc)
mlg_counts = s.mlg_counts
gaps = [x for x in components if x.is_gap]
gapsizes = [None] * len(gaps) # master
for mlg, count in mlg_counts.items():
if count < links:
continue
g = GapEstimator(cc, agp, ob, mlg)
g.compute_all_gaps(minsize=minsize, maxsize=maxsize, \
verbose=verbose)
# Merge evidence from this mlg into master
assert len(g.gapsizes) == len(gaps)
for i, gs in enumerate(gapsizes):
gg = g.gapsizes[i]
if gs is None:
gapsizes[i] = gg
elif gg:
gapsizes[i] = min(gs, gg)
print gapsizes
# Modify AGP
i = 0
for x in components:
if x.is_gap:
x.gap_length = gapsizes[i] or minsize
x.component_type = 'U' if x.gap_length == 100 else 'N'
i += 1
print >> fw, x
fw.close()
reindex([outagpfile, "--inplace"])
