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#!/usr/bin/env lua
--[[
Copyright (c) 2007 Gordon Gremme <gordon@gremme.org>
Copyright (c) 2007 Center for Bioinformatics, University of Hamburg
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.
]]
--[[
convert NCBI reports from file handle <fh> to fasta format and show them on
stdout
The parser is implemented as a state machine with the following states:
- nil
- "parse_identifier"
- "search_sequence"
- "parse_sequence"
- "parse_organism"
]]
function report2fasta(fh, set_organism)
assert(fh)
local state, sequence, description
for line in fh:lines() do
if not state then
if string.match(line, "^IDENTIFIERS") then
state = "parse_identifier"
end
elseif state == "parse_identifier" then
local id = string.match(line, "^GenBank gi:%s*(%d*)")
if id then
description = ">gi|" .. id
state = "search_sequence"
end
elseif state == "search_sequence" then
if string.match(line, "^SEQUENCE") then
state = "parse_sequence"
sequence = ""
end
elseif state == "parse_sequence" then
local sequence_part = string.match(line, "^%s+(%a+)")
if sequence_part then
sequence = sequence..sequence_part
else
assert(sequence.len)
state = "parse_organism"
end
elseif state == "parse_organism" then
local given_organism = string.match(line, "^Organism:%s*(%a.*)")
if given_organism and
(not set_organism or given_organism == set_organism) then
description = description .. " [" .. given_organism .. "]"
io.stdout:write(string.format("%s\n%s\n", description, sequence))
state = nil -- go back to start state
end
end
end
end
local set_organism -- per default, sequences for all organisms are shown
-- argument parsing (XXX: make the option parser more generic)
for i,v in ipairs(arg) do
if v == "-help" then
-- XXX: use basename(arg[0]) insead of arg[0]
io.stderr:write(string.format("Usage: %s [report_file ...]\n", arg[0]))
io.stderr:write("Convert all given report files to fasta files\n\n")
io.stderr:write("-organism set organism to show\n")
io.stderr:write("-help display help and exit\n\n")
io.stderr:write("Report bugs to <gordon@gremme.org>.\n")
os.exit()
elseif v == "-organism" then
if not arg[i+1] then
io.stderr:write("error: missing argument to option -organism\n")
os.exit(1)
end
set_organism = arg[i+1]
table.remove(arg, i+1)
table.remove(arg, i)
end
end
local read_from_stdin = false -- per default, do not read from stdin
-- iterate over all given files
for i,v in ipairs(arg) do
if v == "-" then
read_from_stdin = true
else
local fh, err = io.open(v)
if not fh then
io.stderr:write(string.format("error: %s\n", err))
os.exit(1)
end
report2fasta(fh, set_organism)
fh:close()
end
end
-- finally, read from stdin (if necessary)
if read_from_stdin or not arg[1] then
report2fasta(io.stdin, set_organism)
end
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