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NAME

Bio::SeqAlignment::Components::Sundry Placeholder for miscellaneous components

VERSION

version 0.01

SYNOPSIS

  use Bio::SeqAlignment::Components::Sundry::ComponentName;

DESCRIPTION

This module reserves the name space for miscellaneous components that are relevant for building awesome sequencing applications using the Bio::SeqAlignment framework. The module itself does not provide any functionality, so you will have to load the specific components you need as you build your application, e.g.:

  use Bio::SeqAlignment::Components::Sundry::ComponentName;

where ComponentName is the name of the component you need.

COMPONENTS

Tailing

This module provides functions to add various tails to the 3' of biological sequences. Such modifications are useful for e.g. simulating polyA tails in RNAseq, adding UMI tags to sequences, etc.

DocumentSequenceModifications

This module provides functions to store and retrieve sequence modifications in various formats. These modifications provide a meta-data layer to fasta files (and down the road to fastq files) that can be used to track changes made to the sequences in the file. While there are many ways to store such information, this module provides a simple way to store and retrieve it in common serialization formats (e.g. JSON/YAML/MessagePack). Storing this information in this manner allows for easy retrieval and use in downstream analyses and avoids the use of the rather heavyweight BioPerl modules.

IOHelpers

This module provides helper functions for reading and writing (simple) sequence files. By simple sequence files, we mean files that contain only sequence data, such as FASTA (and some time in the future FASTQ) files. The module uses the BioX::Seq module to parse sequences. This is a simple module that provides a lightweight object-oriented interface to sequence data. It is also wickedly fast.

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.