def main(args):
"""
%prog deltafile refidsfile query.fasta ref.fasta
Plot one query. Extract the references that have major matches to this
query. Control "major" by option --refcov.
"""
p = OptionParser(main.__doc__)
p.add_option("--refcov", default=.01, type="float",
help="Minimum reference coverage [default: %default]")
p.add_option("--all", default=False, action="store_true",
help="Plot one pdf file per ref in refidsfile [default: %default]")
p.set_align(pctid=96, hitlen=500)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
deltafile, refidsfile, queryfasta, reffasta = args
qsizes = Sizes(queryfasta).mapping
rsizes = Sizes(reffasta).mapping
refs = SetFile(refidsfile)
refcov = opts.refcov
pctid = opts.pctid
hitlen = opts.hitlen
deltafile = filter([deltafile, "--pctid={0}".format(pctid),
"--hitlen={0}".format(hitlen)])
if opts.all:
for r in refs:
pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov)
if pdffile:
sh("mv {0} {1}.pdf".format(pdffile, r))
else:
plot_some_queries(refs, qsizes, rsizes, deltafile, refcov)
def main(args):
"""
%prog deltafile
Plot one query. Extract the references that have major matches to this
query. Control "major" by option --refcov.
"""
p = OptionParser(main.__doc__)
p.add_option("--refids", help="Use subset of contigs in the ref")
p.add_option("--refcov", default=.01, type="float",
help="Minimum reference coverage [default: %default]")
p.add_option("--all", default=False, action="store_true",
help="Plot one pdf file per ref in refidsfile [default: %default]")
p.add_option("--color", default="similarity",
choices=("similarity", "direction", "none"),
help="Color the dots based on")
p.add_option("--nolayout", default=False, action="store_true",
help="Do not rearrange contigs")
p.set_align(pctid=0, hitlen=0)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
deltafile, = args
reffasta, queryfasta = open(deltafile).readline().split()
color = opts.color
layout = not opts.nolayout
prefix = op.basename(deltafile).split(".")[0]
qsizes = Sizes(queryfasta).mapping
rsizes = Sizes(reffasta).mapping
refs = SetFile(opts.refids) if opts.refids else set(rsizes.keys())
refcov = opts.refcov
pctid = opts.pctid
hitlen = opts.hitlen
deltafile = filter([deltafile, "--pctid={0}".format(pctid),
"--hitlen={0}".format(hitlen)])
if opts.all:
for r in refs:
pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov,
prefix=prefix, color=color,
layout=layout)
if pdffile:
sh("mv {0} {1}.pdf".format(pdffile, r))
else:
plot_some_queries(refs, qsizes, rsizes,
deltafile, refcov,
prefix=prefix, color=color, layout=layout)
def main(args):
"""
%prog deltafile
Plot one query. Extract the references that have major matches to this
query. Control "major" by option --refcov.
"""
p = OptionParser(main.__doc__)
p.add_option("--refids", help="Use subset of contigs in the ref")
p.add_option("--refcov", default=.01, type="float",
help="Minimum reference coverage [default: %default]")
p.add_option("--all", default=False, action="store_true",
help="Plot one pdf file per ref in refidsfile [default: %default]")
p.add_option("--color", default="similarity",
choices=("similarity", "direction", "none"),
help="Color the dots based on")
p.add_option("--nolayout", default=False, action="store_true",
help="Do not rearrange contigs")
p.set_align(pctid=0, hitlen=0)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
deltafile, = args
reffasta, queryfasta = open(deltafile).readline().split()
color = opts.color
layout = not opts.nolayout
prefix = op.basename(deltafile).split(".")[0]
qsizes = Sizes(queryfasta).mapping
rsizes = Sizes(reffasta).mapping
refs = SetFile(opts.refids) if opts.refids else set(rsizes.keys())
refcov = opts.refcov
pctid = opts.pctid
hitlen = opts.hitlen
deltafile = filter([deltafile, "--pctid={0}".format(pctid),
"--hitlen={0}".format(hitlen)])
if opts.all:
for r in refs:
pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov,
prefix=prefix, color=color,
layout=layout)
if pdffile:
sh("mv {0} {1}.pdf".format(pdffile, r))
else:
plot_some_queries(refs, qsizes, rsizes,
deltafile, refcov,
prefix=prefix, color=color, layout=layout)
def main(args):
"""
%prog deltafile refidsfile query.fasta ref.fasta
Plot one query. Extract the references that have major matches to this
query. Control "major" by option --refcov.
"""
p = OptionParser(main.__doc__)
p.add_option("--refcov",
default=.01,
type="float",
help="Minimum reference coverage [default: %default]")
p.add_option(
"--all",
default=False,
action="store_true",
help="Plot one pdf file per ref in refidsfile [default: %default]")
p.set_align(pctid=96, hitlen=500)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
deltafile, refidsfile, queryfasta, reffasta = args
qsizes = Sizes(queryfasta).mapping
rsizes = Sizes(reffasta).mapping
refs = SetFile(refidsfile)
refcov = opts.refcov
pctid = opts.pctid
hitlen = opts.hitlen
deltafile = filter([
deltafile, "--pctid={0}".format(pctid), "--hitlen={0}".format(hitlen)
])
if opts.all:
for r in refs:
pdffile = plot_some_queries([r], qsizes, rsizes, deltafile, refcov)
if pdffile:
sh("mv {0} {1}.pdf".format(pdffile, r))
else:
plot_some_queries(refs, qsizes, rsizes, deltafile, refcov)
