Pyokit: Python Bio Toolkit

Pyokit is a python library with a collection of tools to make the processing and analysis of high-throughput biological datasets in python a bit easier. This is the Pyokit manual, which describes the library and gives examples of how to use it to achieve common data processing goals. It also contains the developer documentation.

Contents:

• Installing Pyokit
  • Dependencies
  • Installing from PyPI
  • Installing from source
• Using Pyokit
  • Importing Pyokit modules
  • Building user interfaces with Pyokit
    • The CLI class
    • The Option class
  • Genomic Intervals
    • Processing BED files
      • Iterating over BED files
      • Bulk-loading BED files
    • Manipulating Genomic Intervals
      • Collapsing interval sets
      • Intersecting interval sets
      • Searching interval sets
  • Biological Sequences
    • Processing Fasta files
    • Processing FastQ files
    • Manipulating sequences
  • Sequence Alignments
    • Pairwise alignments
      • Pairwise Alignment Meta-data
      • Reading and writing pairwise alignments
  • Retrotransposons
    • Loading annotations
      • Repeatmasker coordinate annotation
      • Repeatmasker full alignments
      • Repeatmasker annotations with on-demand full alignments
    • Liftover
      • Coordinate-only liftover
      • Full-alignment liftover
  • Gene Ontology
  • File indexes
• Pyokit data-structures
  • Genomic Intervals
    • The GenomicInterval class
  • Interval Trees
    • The IntervalTree class
  • Sequences
    • The Sequence class
    • The FastaSequence class
    • The FastqSequence class
  • Sequence Alignments
    • The PairwiseAlignment class
  • Gene Ontology
• Developer documentation
  • Testing your changes
  • Maintaining documentation

Contacts and bug reports

Philip J. Uren

philip.uren@gmail.com

If you found a bug or mistake in this project, I would like to know about it. Before you send me the bug report though, please check the following:

1. Are you using the latest version? The bug you found may already have been fixed.
2. Check that your input is in the correct format and you have selected the correct options.
3. Please reduce your input to the smallest possible size that still produces the bug; I will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be for both of us.

License information

The following applies to this software package and all subparts therein

Pyokit Copyright (C) 2010 - 2015 Philip J. Uren

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 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 GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA

Indices and tables

• Index
• Module Index
• Search Page