A lightweight biological sequence parsing/handling library for Perl 5
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README.md

BioX::Seq

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BioX::Seq is a simple sequence class that can be used to represent biological sequences. It was designed as a compromise between using simple strings and hashes to hold sequences and using the rather bloated objects of Bioperl. Features (or, depending on your viewpoint, bugs) include auto-stringification and context-dependent transformations. It is meant be used primarily as the return object of the BioX::Seq::Stream and BioX::Seq::Fetch parsers, but there may be occasions where it is useful in its own right.

BioX::Seq::Stream and BioX::Seq::Fetch can be used to read in sequence objects in a streaming or random-access fashion from FASTA and FASTQ files.

INSTALLATION

To install this module, run the following commands:

perl Build.PL
./Build
./Build test
./Build install

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for this module with the perldoc command.

perldoc BioX::Seq

LICENSE AND COPYRIGHT

Copyright (C) 2014-2017 Jeremy Volkening jdv@base2bio.com

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

See the LICENSE file in the top-level directory of this distribution for the full license terms.