yabul

Yet Another Bioinformatics Utilities Library

This is a small collection of Python functions for working with protein, DNA, and RNA sequences. We use pandas data frames wherever possible.

Yabul currently supports:

• Reading and writing FASTAs
• Pairwise local and global sequence alignment (uses parasail)

Requires Python 3.6+.

Installation

Install using pip:

$ pip install yabul

You can run the unit from a checkout of the repo as follows:

$ pip install pytest
$ pytest

Example

Reading and writing FASTAs

The read_fasta function returns a pandas.DataFrame:

>>> import yabul
>>> df = yabul.read_fasta("test/data/cov2.fasta")
>>> df.head(3)
                                                             description                                           sequence
id
sp|P0DTC2|SPIKE_SARS2  sp|P0DTC2|SPIKE_SARS2 Spike glycoprotein OS=Se...  MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSS...
sp|P0DTD1|R1AB_SARS2   sp|P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab...  MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHL...
sp|P0DTC1|R1A_SARS2    sp|P0DTC1|R1A_SARS2 Replicase polyprotein 1a O...  MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHL...

The write_fasta function takes (name, sequence) pairs:

>>> yabul.write_fasta("out.fasta", [("protein1", "TEST"), ("protein2", "HIHI")])
>>> yabul.write_fasta("out2.fasta", df.sequence.items())

Sequence alignment

The align_pair function will give a local (Smith-Waterman) and global (Needleman-Wunsch) alignment of two sequences. It returns a pandas.Series with the aligned sequences.

By default, the alignment is global:

>>> yabul.align_pair("AATESTDD", "TEST")
query             AATESTDD
reference         --TEST--
correspondence      ||||
score                   -5
dtype: object

To do a local alignment, pass local=True.

>>> yabul.align_pair("AATESTDD", "TEST", local=True)
query             TEST
reference         TEST
correspondence    ||||
score               19
dtype: object

Dependencies

The alignment routine is a thin wrapper around the Smith-Waterman and Needleman-Wunsch implementations from parasail.

Contributing

We welcome contributions of well-documented code to read and write common bioinformatics file formats using pandas objects. Please include unit tests in your PR. Additional functionality like multiple sequence alignment would also be nice to add.

Releasing

To push a new release to PyPI:

• Make sure the package version specified in __init__.py is a new version greater than what's on PyPI.
• Tag a new release on GitHub matching this version

Travis should deploy the release to PyPI automatically.

Documentation at https://yabul.readthedocs.io/en/latest/ should update automatically on commit.

To build the documentation locally, run:

$ cd docs
$ pip install -r requirements.txt
$ sphinx-build -b html . _build