gt-encseq-sample

#!/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> indexname",
                       oneliner="Extract random substrings from a GtEncseq. ",
                       version="0.1"})
op:option{"-min", action='store', dest='minlen',
                help="minimum length (default: 10)"}
op:option{"-max", action='store', dest='maxlen',
                help="maximum length (default: 100)"}
op:option{"-s", action='store', dest='seed',
                help="random seed (default: time)"}
op:option{"-n", action='store', dest='numstr',
                help="number of substrings (default: 100)"}
options,args = op:parse({numstr = 100, minlen = 10, maxlen = 100, seed=os.time()})

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

if #args < 1 then
  usage()
end

idxname  = args[1]
minlen = tonumber(options.minlen)
maxlen = tonumber(options.maxlen)
nsubstr = tonumber(options.numstr)

math.randomseed(tonumber(options.seed))

el = gt.encseq_loader_new()
es = el:load(idxname)
i = 0
while i < nsubstr do
  len = math.random(minlen, maxlen)
  seqno = math.random(es:num_of_sequences())-1
  eslen = es:seqlength(seqno)
  if eslen > len then
    start = es:seqstartpos(seqno) + math.random(eslen-len)
    stop = start + len - 1
    print(">"..start.."-"..stop.." (length "..len..")")
    print(es:extract_decoded(start, stop))
    i = i + 1
  end
end