gt-toplevelize

#!/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> <sequence> < infile.gff",
                       oneliner="Promote features of a given type to toplevel.",
                       version="0.1"})
op:option{"-t", action='store', dest='type',
                help="type to toplevelize"}
options,args = op:parse({type = "LTR_retrotransposon"})

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

if #args < 1 then
  usage()
end

rm = gt.region_mapping_new_seqfile_matchdescstart(args[1])
gff3v = gt.gff3_visitor_new()
outfile = assert(io.open("toplevelized_" .. options.type .. ".fasta", "w+"))

visitor = gt.custom_visitor_new()
function visitor:visit_feature(fn)
  for node in fn:children() do
    if node:get_type() == options.type then
      outfile:write(">" .. node:get_attribute("ID") .. "\n")
      local seq = node:extract_sequence(options.type, false, rm)
      outfile:write(seq)
      outfile:write("\n")
      local start = node:get_range():get_start()
      local endp = node:get_range():get_end()
      for c in node:children() do
        if c:get_range():get_start() < start or c:get_range():get_end() > endp then
          io.stderr:write(fn:get_type() .. " with ID '"
                        .. tostring(fn:get_attribute("ID")) .. "' has a child "
                        .. c:get_type()
                        .. " outside its coordinates "
                        .. "(" .. tostring(c:get_range())
                        .. " vs. " .. tostring(start)
                        .. "-" .. tostring(endp) ..") on line "
                        .. c:get_line_number() .. ", skipping\n")
          return 0
        else
          local new_rng = gt.range_new(c:get_range():get_start() - start + 1,
                                       c:get_range():get_start() - start +
                                       c:get_range():length())
          c:change_seqid(node:get_attribute("ID"))
          c:set_range(new_rng)
        end
      end
      node:accept(gff3v)
    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
local gn = visitor_stream:next_tree()
while (gn) do
  gn = visitor_stream:next_tree()
end

outfile:close()