https://github.com/chrisarg/alien-seqalignment-edlib

Sequence Alignment tool
https://github.com/chrisarg/alien-seqalignment-edlib

bioinformatics bioinformatics-analysis bioinformatics-scripts sequence-alignment sequencing

Last synced: 7 months ago
JSON representation

Sequence Alignment tool

• Host: GitHub
• URL: https://github.com/chrisarg/alien-seqalignment-edlib
• Owner: chrisarg
• License: other
• Created: 2024-03-10T01:04:17.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-06-14T01:14:30.000Z (over 1 year ago)
• Last Synced: 2025-03-25T11:50:20.988Z (7 months ago)
• Topics: bioinformatics, bioinformatics-analysis, bioinformatics-scripts, sequence-alignment, sequencing
• Language: Perl
• Homepage:
• Size: 43 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: Changes
  • License: LICENSE

Awesome Lists containing this project

README

          
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), , ;

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:

        )

    *   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 

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.