Overview

docs
tests
package

My one-stop-shop for bioinformatics utilities that I have written over the years.

Free software: MIT license

Installation

## Clone the repo
git clone git@github.com:gouinK/kgbio.git

## Navigate to repo
cd kgbio

## To install just utils and helpers
pip install .

## To install seq module
pip install .[seq]

## To install scseq module
pip install .[scseq]

## To install everything
pip install .[seq,scseq]

Documentation

The utils module contains plotting helper functions.

The seq module contains functions related to fastq processing.

The scseq module contains functions related to single-cell-sequencing processing.

utils

-> plotting.py

seq

-> rawdata.py

-> post_aln.py

scseq

-> generalfunctions.py

-> qcfunctions.py

-> dgexfunctions.py

-> populationfunctions.py (work in progress, no guarantees)

-> airrfunctions.py (work in progress, no guarantees)

Not currently active: https://kgbio.readthedocs.io/

Development

Not currently implemented:

To run all the tests run:

tox

Note, to combine the coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox