add_mrna.lua

add_mrna.lua

#!/usr/bin/env gt

function usage()
  io.stderr:write(string.format("Usage: %s <GFF annotation>\n" , arg[0]))
  os.exit(1)
end

if #arg < 1 then
  usage()
end

visitor = gt.custom_visitor_new()
function visitor:visit_feature(fn)
  if fn:get_type() == "gene" then
    new_mrna = gt.feature_node_new(fn:get_seqid(), "mRNA",
                                   fn:get_range():get_start(),
                                   fn:get_range():get_end(),
                                   fn:get_strand())
    fn:add_child(new_mrna)
    new_mrna:set_source(fn:get_source())
    new_mrna:add_attribute("ID", fn:get_attribute("ID") .. ".1")
    for node in fn:children() do
      if node:get_type() == "CDS" then
        fn:remove_leaf(node)
        new_mrna:add_child(node)
      end
    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(arg[1])
visitor_stream.vis = visitor

outstream = gt.gff3_out_stream_new(visitor_stream)
local gn = outstream:next_tree()
while (gn) do
  gn = outstream:next_tree()
end