def neighbor(args):
"""
%prog neighbor agpfile componentID
Check overlaps of a particular component in agpfile.
"""
p = OptionParser(neighbor.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
agpfile, componentID = args
fastadir = "fasta"
cmd = "grep"
cmd += " --color -C2 {0} {1}".format(componentID, agpfile)
sh(cmd)
agp = AGP(agpfile)
aorder = agp.order
if not componentID in aorder:
print(
"Record {0} not present in `{1}`.".format(componentID, agpfile),
file=sys.stderr,
)
return
i, c = aorder[componentID]
north, south = agp.getNorthSouthClone(i)
if not north.isCloneGap:
ar = [north.component_id, componentID, "--dir=" + fastadir]
if north.orientation == "-":
ar += ["--qreverse"]
overlap(ar)
if not south.isCloneGap:
ar = [componentID, south.component_id, "--dir=" + fastadir]
if c.orientation == "-":
ar += ["--qreverse"]
overlap(ar)
def neighbor(args):
"""
%prog neighbor agpfile componentID
Check overlaps of a particular component in agpfile.
"""
p = OptionParser(neighbor.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
agpfile, componentID = args
fastadir = "fasta"
cmd = "grep"
cmd += " --color -C2 {0} {1}".format(componentID, agpfile)
sh(cmd)
agp = AGP(agpfile)
aorder = agp.order
if not componentID in aorder:
print >> sys.stderr, "Record {0} not present in `{1}`."\
.format(componentID, agpfile)
return
i, c = aorder[componentID]
north, south = agp.getNorthSouthClone(i)
if not north.isCloneGap:
ar = [north.component_id, componentID, "--dir=" + fastadir]
if north.orientation == '-':
ar += ["--qreverse"]
overlap(ar)
if not south.isCloneGap:
ar = [componentID, south.component_id, "--dir=" + fastadir]
if c.orientation == '-':
ar += ["--qreverse"]
overlap(ar)
