Lua: for scripting OBITools

Lua: the scripting language for OBITools #

Lua is a scripting language. Its name means moon in Portuguese. Its purpose is to provide an interpreter that can be easily integrated into software to add scripting capabilities. OBITools provides the obiscript command for this purpose. The obiscript command allows a small script to be applied to each selected sequence in a sequence file. The Lua interpreter used by obiscript is GopherLua Version 1.1.1 which implements Lua version 5.1.

The aim of this section is not to be a full introduction to Lua, but to show how to write a Lua script that can be used with obiscript . A full documentation of Lua is available on the official website of the language ( https://www.lua.org/manual/5.1).

The structure of a Lua script for obiscript #

📄 example.lua
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17

function begin()
    obicontext.item("compteur",0)
end

function worker(sequence)
    samples = sequence:attribute("merged_sample")
    samples["tutu"]=4
    sequence:attribute("merged_sample",samples)
    sequence:attribute("toto",44444)
    nb = obicontext.inc("compteur")
    sequence:id("seq_" .. nb)
    return sequence
end

function finish()
    print("compteur = " .. obicontext.item("compteur"))
end

The begin and finish function #

The worker function #

The obicontext to share information #

The OBITools classes #

The BioSequence class #

The BioSequenceSlice class #

The Taxonomy class #

The Taxon class #

Dealing with the OBITools4 multithreading #

📄 extrem_quality.lua
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59

--
-- Script for obiscript extracting the qualities of
-- the first `size` and last `size` base pairs of 
-- all the reads longer than 2 x `size`
--
-- The result is a csv file on the stdout
--
-- obiscript -S ../qualities.lua FAZ61712_c61e82f1_69e58200_0_nolambda.fastq > xxxx

-- Import the io module
local io = require("io")

-- Set the output stream to the stdout of the Go program
io.output(io.stdout)

size = 60

function begin()
    obicontext.item("locker", Mutex:new())
    header = "id"
    for i = 1, size do
        header = header .. ", L" .. i 
    end


    for i = size, 1, -1 do
        header = header .. ", R" .. i
    end

    obicontext.item("locker"):lock()
    print(header)
    obicontext.item("locker"):unlock()

end

function worker(sequence)
    l = sequence:len()

    if l > size * 2 then
    qualities = sequence:qualities()
    rep = sequence:id()

    for i = 1, size do
        rep = rep .. ", " .. qualities[i]
    end

    for i = size, 1, -1 do
        rep = rep .. ", " .. qualities[l - i + 1]
    end

    obicontext.item("locker"):lock()
    print(rep)
    obicontext.item("locker"):unlock()

    end

    return BioSequenceSlice.new()

end