gt-stripstop

#!/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 <sequence file> < infile.gff",
                       oneliner="Converts all genes with internal stop codons "
                                .. "to pseudogenes.",
                       version="0.1"})
op:option{"-r", action='store_true', dest='remove',
                help="skip feature instead of making it a pseudogene"}
options,args = op:parse({remove = false})

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

region_mapping = gt.region_mapping_new_seqfile_matchdescstart(args[1])

outvis = gt.gff3_visitor_new()

visitor = gt.custom_visitor_new()
visitor.last_seqid = nil
function visitor:visit_feature(fn)
  local has_stop = false
  local protseq = nil
  for node in fn:children() do
    if node:get_type() == "mRNA" then
      protseq = node:extract_and_translate_sequence("CDS", true,
                                                          region_mapping)
      if protseq:sub(1, -2):match("[*+#]") then
        has_stop = true
        break
      end
    end
  end
  -- make this a pseudogene
  if has_stop then
    if not options.remove then
      local npseudogene = nil
      local nptranscript = nil
      local npexon = nil
      for node in fn:children() do
        local rng = node:get_range()
        if node:get_type() == "gene" then
          npseudogene = gt.feature_node_new(node:get_seqid(), "pseudogene",
                                            rng:get_start(), rng:get_end(),
                                            node:get_strand())
          for k,v in node:attribute_pairs() do
            npseudogene:set_attribute(k, v)
          end
          npseudogene:set_attribute("has_internal_stop", "true")
          local rorth = npseudogene:get_attribute("ratt_ortholog")
          if rorth and protseq then
            npseudogene:set_attribute("Target", rorth .. " 1 " .. string.len(protseq))
          end
        elseif node:get_type() == "mRNA" then
          assert(npseudogene)
          nptranscript = gt.feature_node_new(node:get_seqid(),
                                             "pseudogenic_transcript",
                                             rng:get_start(), rng:get_end(),
                                             node:get_strand())
          npseudogene:add_child(nptranscript)
          for k,v in node:attribute_pairs() do
            nptranscript:set_attribute(k, v)
          end
        elseif node:get_type() == "CDS" then
          assert(nptranscript)
          npexon = gt.feature_node_new(node:get_seqid(),
                                       "pseudogenic_exon",
                                       rng:get_start(), rng:get_end(),
                                       node:get_strand())
          nptranscript:add_child(npexon)
          for k,v in node:attribute_pairs() do
            npexon:set_attribute(k, v)
          end
        end
      end
      if npseudogene then
        npseudogene:accept(outvis)
      end
    end
  else
    fn:accept(outvis)
  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
local gn = visitor_stream:next_tree()
while (gn) do
  gn = visitor_stream:next_tree()
end