gt-ltrclean

#!/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.
]]

math.randomseed(os.time())
package.path = gt.script_dir .. "/?.lua;" .. package.path
require("optparse")

op = OptionParser:new({usage="%prog <options> < infile.gff3",
                       oneliner="Keep only 'best' (smallest e-value) protein "
                         .. "match per overlapping cluster from LTRdigest "
                         .. "results.",
                       version="0.1"})
op:option{"-type", action='store', dest='type',
                help="root type (default: LTR_retrotransposon)"}
options,args = op:parse({type = 'LTR_retrotransposon'})

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

visitor = gt.custom_visitor_new()
function visitor:visit_feature(fn)
  local retrotransposons = {}
  -- collect LTR_retrotransposon nodes
  for node in fn:children() do
    if node and node:get_type() == options.type then
      table.insert(retrotransposons, node)
    end
  end
  for _,node in ipairs(retrotransposons) do
    -- determine clusters of overlapping matches
    local ovlclusters = {}
    for node2 in node:children() do
      if node2 and node2:get_type() == "protein_match" then
        local inserted = false
        for _, cl in ipairs(ovlclusters) do
          for _, n in ipairs(cl) do
            if n:get_range():overlap(node2:get_range()) then
              table.insert(cl, node2)
              inserted = true
              break
            end
          end
        end
        if not inserted then
          table.insert(ovlclusters, {node2})
        end
      end
    end
    for _,cl in pairs(ovlclusters) do
      -- sort clusters by ascending e-value (feature score)
      table.sort(cl, function (a,b)
       local as = a:get_score()
       if not as then
         as = 1000
       end
       local bs = a:get_score()
       if not bs then
         bs = 1000
       end
       return as < bs
      end)
      -- keep only best element
      for i,n in ipairs(cl) do
        -- best element is the first, get rid of all others
        if i > 1 then
          node:remove_leaf(n)
        end
      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 gets its input from GFF3 input file
visitor_stream.instream = gt.gff3_in_stream_new_sorted()
visitor_stream.vis = visitor

-- output stream prints features in GFF3
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