Biopython

Biopython is an open source set of tools for biological computation written in Python by an international team of developers.

Different modules extend Biopython's capabilities to include many biological features such as:

• Sequence Annotation          Genome Diagrams          Machine Learning
• Phylogeny          Population Genetics          Protein Structure

Tools

Python3.6 upwards

• Must be compatible with all recent versions of Python

Flake8

• Style guide enforcement to follow PEP 8 guidelines

Git & GitHub

• Version control
• PRs and communication

Pull Requests

#3309 : Utilized __slots__ in Seq and SeqRecord classes

Open Pull Request
New Feature


• Added __slots__ to the Seq and SeqRecord classes. In SeqRecord the seq and letter_annotations attributes were changed into functions with property decorators.
Read more on Github...

#3307 : Removed partial codon warning when testing amino acid sequences

Open Pull Request
Bug Fix


• Only changed the testing amino acid sequences so the warning isn't triggered. Amino acid sequences don't need to be divisible by 3, only codon sequences. Trimmed three testing protein_seqs by one amino acid to prevent irrelevant partial codon warning from appearing when testing TranslationError of amino acid Seq() object.
Read more on Github...

#1973 : Fix for Bio.motifs.jaspar.db DocTests

Merged Pull Request
Wrote Tests
Bug Fix


• Change of doctests for the JASPAR5 class into RST literal block, and update the example to reflect the new JASPAR2018 mysqldump data.
Read more on Github...

#1967 : Fix for Bio.motifs.mast and Bio.motifs.minimal DocTests

Merged Pull Request
Bug Fix


• Correction of doctests for the Bio.motifs.mast and Bio.motifs.minimal class. Allows users to have workable examples.
Read more on Github...

#1942 : Enhance CodonAlignment to support addition operation

Merged Pull Request
New Feature
Wrote Tests


• Collaborated with an experienced contributor, @zruan, to add the __add__() feature to the CodonAlignment class.
• Wrote unitests to ensure appropriate sequence alphabet compatibility between CodonAlignment and MultipleSeqAlignment objects.
• Debugged and contributed to each others code.
Read more on Github... And here... And here...

#1937 : Fix for Bio.motifs.meme DocTests

Merged Pull Request
Wrote Tests
Bug Fix


• Correction of doctests for the Bio.motifs.meme class. Allows users to have workable examples.
Read more on Github...

#1747 : Removes files created during run of test_Tutorial.py

Merged Pull Request
Bug Fix


• Fix to ensure proper cleanup of all temporary files after testing is completed.
Read more on Github...

#1731 : Added the Seq.join() method

Merged Pull Request
New Feature
Wrote Tests


• Addition of the new feature join() to the Seq, MutableSeq and UnknownSeq classes. This feature allows the concatenation of biological sequences of comparable types. Following inspiration from Pythons String join() method.
• Thorough Unittests created to ensure function in appropriate cases and failure in instances with usage of incompatible objects.
• Active discussion with the maintainer @peterjc to ensure desired functionality and received guidance as a first time contributor.
Read more on Github... And here...