https://github.com/chrisarg/bio-seqalignment-components-sundry

Various components for building RNA sequencing applications in Perl
https://github.com/chrisarg/bio-seqalignment-components-sundry

bioinformatics fasta fastq rna-seq sequence-alignment sequencing

Last synced: 7 months ago
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Various components for building RNA sequencing applications in Perl

• Host: GitHub
• URL: https://github.com/chrisarg/bio-seqalignment-components-sundry
• Owner: chrisarg
• License: other
• Created: 2024-04-22T02:48:51.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-06-09T16:47:04.000Z (over 1 year ago)
• Last Synced: 2025-03-25T11:50:20.969Z (7 months ago)
• Topics: bioinformatics, fasta, fastq, rna-seq, sequence-alignment, sequencing
• Language: Perl
• Homepage:
• Size: 24.4 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README
  • Changelog: Changes
  • License: LICENSE

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README

          
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 

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.