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Bio-SeqAlignment-Components-Libraries-edlib-0.03
River stage zero No dependents
/ Bio::SeqAlignment::Components::Libraries::edlib

NAME

Bio::SeqAlignment::Components::Libraries::edlib - edlib library for developing sequence alignment tools

VERSION

version 0.03

SYNOPSIS

  use Bio::SeqAlignment::Components::Libraries::edlib;
  my $ffi = Bio::SeqAlignment::Components::Libraries::edlib->new_edlib_aligner();
  my $configuration = Bio::SeqAlignment::Components::Libraries::edlib->configure_edlib_aligner( $ffi, %config );
  my $align = Bio::SeqAlignment::Components::Libraries::edlib->edlibAlign( $query_seq, $query_len, $ref_seq, $ref_seq_len, $configuration->{edlib_config} );
  Bio::SeqAlignment::Components::Libraries::edlib->edlibFreeAlignResult( $align );

DESCRIPTION

This module provides a Perl interface to the edlib library for developing sequence alignment tools. The edlib library is a C/C++ library for sequence alignment using edit distance. It supports three alignment modes: global (Needleman-Wunsch), semi-global, and local (Smith-Waterman). This module provides a Perl interface to the edlib library for developing sequence alignment tools. This particular module is meant to be used as a component in a larger sequence alignment tool, e.g. one that combines a Linear dataflow and a generic sequence mapper. Currently only the alignment score is returned. Future versions will include the alignment path and the alignment locations in order to handle multiple/overlapping hits.

METHODS

new_edlib_aligner

  my $ffi = Bio::SeqAlignment::Components::Libraries::edlib->new_edlib_aligner();

This method creates a new FFI::Platypus object that can be used to call the functions from the edlib library. The FFI::Platypus object is returned.

configure_edlib_aligner

  my $configuration = Bio::SeqAlignment::Components::Libraries::edlib->configure_edlib_aligner( $ffi, %config );

This method configures the edlib aligner with the specified configuration. The configuration is passed as a hash with the following keys: mode, task, filter, additionalEqualities, and additionalEqualitiesLength. The configuration is returned as a hash reference with two keys: edlib_config and align_config. The edlib_config key contains the configuration for the edlib aligner, while the align_config key contains the configuration for the alignment.

edlibAlign

  my $align = Bio::SeqAlignment::Components::Libraries::edlib->edlibAlign( $query_seq, $query_len, $ref_seq, $ref_seq_len, $configuration->{edlib_config} );

This method performs the sequence alignment using the edlib library. It takes as input the query sequence, the length of the query sequence, the reference sequence, the length of the reference sequence, and the configuration for the edlib aligner. It returns the alignment result as a hash reference.

edlibFreeAlignResult

  Bio::SeqAlignment::Components::Libraries::edlib->edlibFreeAlignResult( $align );

This method frees the memory allocated for the alignment result.

EXPORTS

The following constants are exported by default:

  • EDLIB_STATUS_OK

  • EDLIB_STATUS_ERROR

The following functions are exported by the 'functions' tag:

  • configure_edlib_aligner

  • edlibNewAlignConfig

  • edlibAlign

  • edlibFreeAlignResult

  • new_edlib_aligner

The following records are exported by the 'records' tag:

  • EdlibEqualityPair

  • EdlibAlignResult

  • EdlibAlignConfig

SEE ALSO

TODO

  • Add support for obtaining/parsing the alignment path

  • Add support for obtaining/parsing the alignment locations

  • Add support for mapping multiple and/or overlapping hits

AUTHOR

Christos Argyropoulos <chrisarg@cpan.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2024 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.