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https://github.com/gf712/abpytools

Python package for analysis of antibody heavy and light chains
https://github.com/gf712/abpytools

antibody antibody-numbering antibody-sequences bioinformatics python

Last synced: about 2 months ago
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Python package for analysis of antibody heavy and light chains

Host: GitHub
URL: https://github.com/gf712/abpytools
Owner: gf712
License: mit
Created: 2017-01-18T12:28:14.000Z (almost 8 years ago)
Default Branch: master
Last Pushed: 2020-08-16T09:39:12.000Z (over 4 years ago)
Last Synced: 2024-10-02T22:16:50.557Z (3 months ago)
Topics: antibody, antibody-numbering, antibody-sequences, bioinformatics, python
Language: Python
Homepage: https://gf712.github.io/AbPyTools/
Size: 894 KB
Stars: 23
Watchers: 2
Forks: 3
Open Issues: 3
Metadata Files:
- Readme: README.md
- License: LICENSE.txt

Awesome Lists containing this project

README

        AbPyTools

=========

[![Coverage Status](https://coveralls.io/repos/github/gf712/AbPyTools/badge.svg?branch=master)](https://coveralls.io/github/gf712/AbPyTools?branch=master)

[![Build Status](https://travis-ci.org/gf712/AbPyTools.svg?branch=master)](https://travis-ci.org/gf712/AbPyTools)

[![Code Health](https://landscape.io/github/gf712/AbPyTools/master/landscape.svg?style=flat)](https://landscape.io/github/gf712/AbPyTools/master)

[![Documentation Status](https://readthedocs.org/projects/abpytools/badge/?version=latest)](https://abpytools.readthedocs.io/en/latest/?badge=latest)

AbPyTools is a Python 3 package to extract information from heavy and light antibody chain sequences. Using the built-in

Antibody and ChainCollection it is very easy to manipulate the data and do more specific analysis with custom scripts.

This package is still in its early days and and lacks detailed documentation...!

Below are some existing features and some planned future additions.

At the moment it is updated several times a day until I am happy with the base functions. In the future the development 

will be performed in a separate branch.

AbPyTools features

- 

- obtain Antibody numbering by querying AbNum (http://www.bioinf.org.uk/abs/abnum/)

- analysis of scFv sequences with optimised backend

- higher level class that can load data from several antibody sequences

  - load and write antibody sequences in FASTA and json formats

  - calculates hydrophobicity matrix for whole dataset

  - get all the data already mentioned above

  - access CDR and framework sequences

- Work with heavy and light chains or combinations 

- high level function to easily plot CDR length using a FASTA file as input

Stuff that will be added/ worked on next

- 

- Add remaining antibody numbering schemes

- write tutorials

- adding some useful functions, such as comparing sequence with available datasets

- write high level code for more specific analysis

  - plot CDR lengths of antibodies

  

Cython

-

From version 0.3 AbPyTools will start using Cython to speed up numerical manipulations.

In the front end nothing will change, but installation from source will require Cython!

This new feature will speed up most calculations significantly. The backend uses code written 

from scratch that mimics numpy behaviour but runs much faster, since it is more specialised and lightweight.

Installing abpytools

-

## From source

Clone code from the GitHub repository

`git clone https://github.com/gf712/AbPyTools.git`

Change to package directory in your local machine

`cd path/to/AbPyTools`

Install package

`python setup.py install`

Run tests (recommended)

`python setup.py test`

## From pypi

`pip install abpytools` 

Import to python

-

`import abpytools`

Changelog

-

### v0.3.2 (release date 31/10/2018)

 - Added docs page

 - Fixed Pypi build with Cython files

### v0.3.1 (release date 30/10/2018)

 - Major:

   - Protobuf support to serialise core objects (`ChainCollection` and `FabCollection`)

     - speed up in saving and loading large files

     - files are about 5 times smaller

   - Dropped support for Python 3.5 to start using f-strings

   - API changes:

     - Cleaned up object instantiation and added factory functions (**This will break some old code but provides a cleaner iterface**)

 - Minor:

   - added Python 3.7 to Travis script (also dropped Python 3.5)

### v0.3 (release date 11/10/2018):

 - Implementation of backend calculations with Cython leading to speedups of several orders of magnitude