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#!/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.
]]
function usage()
io.stderr:write("Creates artificial test sequences for TIRvish.\n")
io.stderr:write(string.format("Usage: %s <prefix>\n" , arg[0]))
os.exit(1)
end
if #arg < 1 then
usage()
end
prefix = arg[1]
totallen = 10000000
nof_tirs = 40
tirmin, tirmax = 200, 400
tirlmin, tirlmax = 1000, 6000
tsdmin, tsdmax = 6, 10
BASES = {'a','c','g','t'}
math.randomseed(os.time())
function revcomp(str)
return string.gsub(str, "[acgt]",
{a = "t", c = "g", g = "c", t = "a"}):reverse()
end
function make_dna_of_len(l)
out = {}
for i = 1,l do
out[i] = BASES[math.random(#BASES)]
end
return table.concat(out)
end
function make_tir()
tirlen = tirmin + math.random(tirmax-tirmin)
elem_len = tirlmin + math.random(tirlmax-tirlmin)
tsdlen = tsdmin + math.random(tsdmax-tsdmin)
tsd = make_dna_of_len(tsdlen)
tir = make_dna_of_len(tirlen)
elem_seq = tsd .. tir .. make_dna_of_len(elem_len-2*tirlen) ..
revcomp(tir) .. tsd
return elem_seq, string.len(elem_seq), tirlen, tir, revcomp(tir), tsdlen
end
base_seq = make_dna_of_len(totallen)
local annfile = assert(io.open(arg[1] .. ".gff3", "w+"))
seq = base_seq
for i = 1, nof_tirs do
pos = math.random(string.len(seq)-1)
elem_seq, elem_len, tirlen, tir, revtir, tsdlen = make_tir()
annfile:write(prefix .."\t.\t" .. pos .. "\t" .. pos + elem_len -1 .. "\t"
.. ".\t+\t.\t")
left = string.sub(seq, 1,pos)
right = string.sub(seq, pos+1)
seq = left .. elem_seq .. right
end
annfile:close()
local seqfile = assert(io.open(arg[1] .. ".fasta", "w+"))
seqfile:write(">" .. prefix .. "\n")
seqfile:write(seq)
seqfile:write("\n")
seqfile:close()
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