NAME

Alien::SeqAlignment::edlib - find, build and install the edlib library

VERSION

version 0.10

SYNOPSIS

To execute the alignment using the command line tool:

use Alien::SeqAlignment::edlib;
use Env qw( @PATH );

unshift @PATH, Alien::SeqAlignment::edlib->bin_dir;
system Alien::SeqAlignment::edlib->edlib_aligner, (list of options), <queries.fasta>, <target.fasta>;

DESCRIPTION

This distribution provides edlib so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the edlib github repo, and if that fails it will use the location of a fork but the author of this module. Contrary to other Alien modules, this one will not test for a prior install of the edlib library, but will install from source into a private share location for the use by other modules. This strategy will avoid overwritting prior system installs of the edlib library, and is guaranteed to use the latest version of edlib. The build provides the static and shared libraries, but also the CLI aligner (edlib-aligner, not currently available in Windows).

METHODS

edlib_aligner

Alien::SeqAlignment::edlib->edlib_aligner

Returns the command name for running the CLI version of the edlib aligner Since the command line tool is not built under Windows by the edlib project make files, this method will return undef under Windows.

USAGE

Command line tool

use v5.38;
use Alien::SeqAlignment::edlib;
use Env qw( @PATH );

unshift @PATH, Alien::SeqAlignment::edlib->bin_dir;
my $string1 =      "ACGACG";
my $string2 = "CCCCCACGTCG";

# save sequences
open my $fh, '>', 'seq1.fasta';
say $fh ">Seq1\n$string1";
close $fh;
open my $fh, '>', 'seq2.fasta';
say $fh ">Seq2\n$string2";
close $fh;

system Alien::SeqAlignment::edlib->edlib_aligner, '-m', 'HW','-n','0', '-k','-1','-p','-f' ,'NICE','seq1.fasta', 'seq2.fasta';

Output

    Using HW alignment mode.
    Reading queries...
    Read 1 queries, 6 residues total.
    Reading target fasta file...
    Read target, 11 residues.

    Comparing queries to target...

    Query #0 (6 residues): score = 1
    T: ACGTCG (5 - 10)
       ||| ||
    Q: ACGACG (0 - 5)

SEE ALSO

• edlib

  Edlib is a lightweight and superfast C/C++ library for sequence alignment using the edit (Levenshtein) distance between two or more biological (usually) sequences. It can calculate the edit distance, find the optimal aligment path and the coordinates (start/end) locations. It supports multiple alignment modes such as global (NW), prefix (SHW) and infix (HW). The library does not handle utf8 and its primary use is to compute edit distances and alignments over small (255 characters or fewer) alphabets as they occur in bioinformatic applications.

• Text::Levenshtein::Edlib

  An XS library that also wraps around the edlib library and returns edit distances, as well as alignment paths.

• Text::Levenshtein::XS

  An XS library that computes edit distances but not alignment paths. See also its github repository at: https://github.com/ugexe/Text--Levenshtein--XS/)

• Text::LevenshteinXS

  Yet another XS implementation of Levenshtein distance over strings (no alignment path).

• Alien

  Documentation on the Alien concept itself.

• Alien::Base

  The base class for this Alien. The methods in that class allow you to use the static and the dynamic edlib library in your code.

• Alien::Build::Manual::AlienUser

  Detailed manual for users of Alien classes.

• Bio::SeqAlignment

  A collection of tools and libraries for aligning biological sequences from within Perl.

AUTHOR

Christos Argyropoulos chrisarg@gmail.com

COPYRIGHT AND LICENSE

This software is copyright (c) 2023 by Christos Argyropoulos.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.