bnemoz/abutils

abutils

Models and general-purpose utilities for working with antibody repertoire data. abutils is a core component of the ab[x] toolkit for antibody sequence analysis.

• Source code: github.com/briney/abutils
• Documentation: abutils.readthedocs.org
• Download: pypi.python.org/pypi/abutils
• Docker: hub.docker.com/r/briney/abstar/

install

pip install abutils

api

The intended use of abutils is through the public API, enabling incorporation of abutils' methods and utilities into integrated analysis pipelines, other standalone software tools, or for interative analysis of antibody repertoires. See the abutils documentation for more detail about the API.

testing

To run the test suite, clone or download the repository and run pytest ./ from the top-level directory. The same tests are run after every commit using TravisCI.

requirements

Python 3.6+
biopython
celery
ete3
matplotlib
numpy
nwalign3
pandas
paramiko
pymongo
pytest
scikit bio
seaborn

All of the above dependencies can be installed with pip, and will be installed automatically when installing abstar with pip.
If you're new to Python, a great way to get started is to install the Anaconda Python distribution, which includes pip as well as a ton of useful scientific Python packages.

abutils has a few additional non-python dependencies that are not required for installation but are necessary for specific functions:

• abutils.alignment.mafft requires MAFFT
• abutils.mongodb.mongoimport requires MongoDB
• abutils.phylogeny.fasttree requires FastTree
• abutils.phylogeny.igphyml requires IgPhyML
• abutils.phylogeny.lsd requires LSD
• abutils.s3 requires s3cmd