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.
To install this module, run the following commands:
git clone https://github.com/jvolkening/p5-BioX-Seq.git
cd p5-BioX-Seq
perl Build.PL
./Build
./Build test
./Build install
Or, with cpanminus:
cpanm BioX::Seq
Or, with conda:
conda install -c bioconda perl-biox-seq
After installing, you can find documentation for this module with the perldoc command.
perldoc BioX::Seq
Copyright (C) 2014-2020 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.