gt-TEMPLATE

#!/usr/bin/env gt

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

op = OptionParser:new({usage="%prog <options> < infile.gff",
                       oneliner="Do something with an input GFF.",
                       version="0.1"})
op:option{"-x", action='store_true', dest='my_bool',
                help="a boolean option"}
op:option{"-s", action='store', dest='something',
                help="some string input"}
options,args = op:parse({my_bool = false, something = "foo"})

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

if #args < 1 then
  usage()
end

visitor = gt.custom_visitor_new()
function visitor:visit_feature(fn)
  for node in fn:children() do
    if node:get_type() == "exon" then
       -- do stuff
    elseif node:get_type() == "intron" then
       -- do stuff
    end
  end
  return 0
end

-- make simple visitor stream, just applies given visitor to every node
visitor_stream = gt.custom_stream_new_unsorted()
function visitor_stream:next_tree()
  local node = self.instream:next_tree()
  if node then
    node:accept(self.vis)
  end
  return node
end

visitor_stream.instream = gt.gff3_in_stream_new_sorted()
visitor_stream.vis = visitor
out_stream = gt.gff3_out_stream_new_retainids(visitor_stream)
local gn = out_stream:next_tree()
while (gn) do
  gn = out_stream:next_tree()
end