gt-bequeath

#!/usr/bin/env gt

--[[
  Copyright (c) 2015 Sascha Steinbiss <sascha@steinbiss.name>

  Permission to use, copy, modify, and distribute this software for any
  purpose with or without fee is hereby granted, provided that the above
  copyright notice and this permission notice appear in all copies.

  THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
  WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
  MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
  ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
  WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
  ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
  OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
]]

package.path = gt.script_dir .. "/?.lua;" .. package.path
require("optparse")

op = OptionParser:new({usage="%prog <options> < infile.gff",
                       oneliner="Adds a given parent attribute to "
                                .. "all child features.",
                       version="0.1"})
op:option{"-a", action='store', dest='attribute',
                help="attribute to pass on to children (default: Name)"}
options,args = op:parse({attribute = "Name"})

function usage()
  op:help()
  os.exit(1)
end

function apply_to_child(root, attr, value)
  for v in root:direct_children() do
  	local a = v:get_attribute(attr)
  	if a then
  	  value = a
  	end
  	if value and not a then
  	  v:set_attribute(attr, value)
  	end
  	apply_to_child(v, attr, value)
  end
end

add_child_visitor = gt.custom_visitor_new()
function add_child_visitor:visit_feature(fn)
  apply_to_child(fn, options.attribute, fn:get_attribute(options.attribute))
end

vis_stream = gt.custom_stream_new_unsorted()
function vis_stream:next_tree()
  local node = self.instream:next_tree()
  if node then
  	node:accept(add_child_visitor)
  end
  return node
end

in_stream = gt.gff3_in_stream_new_sorted()
vis_stream.instream = in_stream
out_stream = gt.gff3_out_stream_new(vis_stream)

local gn = out_stream:next_tree()
while (gn) do
  gn = out_stream:next_tree()
end