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math.randomseed(os.time())
function usage()
io.stderr:write(string.format("Usage: %s indexname minlen maxlen n_substr\n", arg[0]))
io.stderr:write("Extract <nof_substr> random substrings from a GtEncseq.\n")
os.exit(1)
end
if #arg == 4 then
idxname = arg[1]
minlen = tonumber(arg[2])
maxlen = tonumber(arg[3])
nsubstr = tonumber(arg[4])
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
else
usage()
end
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