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function usage()
io.stderr:write(string.format("Usage: %s file\n", arg[0]))
io.stderr:write("Checks a GFF file for line-sortedness.\n")
os.exit(1)
end
function split(str, sep)
local fields = {}
str:gsub("([^"..sep.."]*)"..sep, function(c) table.insert(fields, c) end)
return fields
end
if #arg == 1 then
gfffile = arg[1]
else
usage()
end
cur_seqid = nil
cur_pos = 0
file = assert(io.open(gfffile, "r"))
i = 0
for line in file:lines() do
i = i + 1
if string.match(line, "^##FASTA") then
break
end
if not string.match(line, "^#") then
f = split(line, "\t")
if #f < 5 then
io.stderr:write("Not enough fields in line " .. i .. "\n")
os.exit(1)
end
seqid, startpos, endpos = f[1], f[4], f[5]
if seqid ~= cur_seqid then
cur_seqid = seqid
cur_pos = 0
end
if tonumber(startpos) < cur_pos then
io.stderr:write("Error: " .. startpos .. " < "
.. cur_pos .. " (line " .. i ..")\n")
io.stderr:write(line .. "\n")
os.exit(1)
end
cur_pos = tonumber(startpos)
end
end
file:close()
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