bio_utils: library of common bioinformatic functions

Authors:Alex Hyer, William Brazelton, Christopher Thornton Date:Dec 26, 2018 Version:1.3

Software library containing common bioinformatic functions

Copyright:

__init__.py software library containing common bioinformatic functions Copyright (C) 2015 William Brazelton, Alex Hyer

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

This program 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 GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.

Summary

bio_utils is a library of Python modules performing routine functions in bioinformatic scripts.

Introduction

Many bioinformatic scripts perform similar or identical tasks internally during the execution of a program. Such tasks include reading FASTA files or filtering BLAST+ results. bio_utils contains numerous functions that quickly and simply handle simple, mundane, everyday tasks in a streamlined and simple fashion to save developers time. bio_utils aims to be as simple as possible, providing functionality without adding in unnecessary features, i.e. bio_utils is as vanilla as reasonable. This both increases the speed of most functions and greatly simplifies APIs.

Many libraries, such as SCREED and Biopython, already provide importable functions that execute these simple tasks. SCREED maintains a fairly simple API but is fairly slow and no one has updated the original repo since 2012-06-17. Numerous developers actively maintain Biopython and it is quite a bit faster, in some regards, than SCREED. However, Biopython stocks their functions with an enormous number of features that, while useful in a Python interpreter, are often ignored by programs or can be accomplished more quickly using built-in Python features, i.e. Biopython is bloatware to many developers. As aforementioned, bio_utils’ vanilla design overcomes both these libraries issues by providing both simplicity and speed.

At this point in time, bio_utils is quite small and its scope limited. The authors intend to slowly but surely increase this library’s repertoire over time. We welcome any and all contributions to our project.

Installation

pip install bio_utils

Contents

• Classes
  • Introduction
  • B6Entry
  • FastaEntry
  • FastqEntry
  • GFF3Entry
  • SamEntry
• Iterators
  • Introduction
  • Common Features
  • b6_iter
  • fasta_iter
  • fastq_iter
  • gff3_iter
  • sam_iter
• Verifiers
  • Introduction
  • entry_verifier
  • b6_verifier
  • binary_guesser
  • fasta_verifier
  • fastq_verifier
  • gff3_verifier
  • sam_verifier
• Blast Tools
  • Introduction
  • blast_to_cigar
  • b6_evalue_filter
  • query_sequence_retriever
  • subject_sequence_retriever
• Contributing
  • Introduction
  • How to Contribute
  • Core Principles
  • Script Requirements
  • Sub-Package Requirements
• Roadmap
  • Introduction
  • V1.1
  • V1.2
  • V2.0

Indices and tables

• Index
• Module Index
• Search Page

Copyright

bio_utils’ operates under the GPLv3 License and may be edited and redistributed as per that license.