abutils

Models, functions and visualization tools for working with adaptive immune receptore repertoire (AIRR) data. The primary purpose of abutils is to provide generalizable tools suitable for direct use analyzing bulk AIRR datasets, and is used by scab for single cell AIRR analysis. abutils is a core component of the ab[x] toolkit for AIRR data analysis.

• Source code: github.com/briney/abutils
• Documentation: abutils.readthedocs.org
• Download: pypi.python.org/pypi/abutils

install

pip install abutils

api

We've tried to design the abutils API to be intuitive yet powerful, with the goal of enabling both interactive analyses (via environments like Jupyter notebooks) as well as integration of abutils tools into more complex analysis pipelines and/or standalone software tools. See the documentation for more detail about the API. As always, any feedback is greatly appreciated!!

testing

You can run the complete abutils test suite by first installing pytest:

pip install pytest

followed by:

git clone https://github.com/briney/abutils
cd abutils
pytest

This test suite is automatically run following every commit, and is tested against all supported versions of Python.

requirements

python 3.8+

abstar
baltic
biopython
celery
ete3
fastcluster
matplotlib
mnemonic
natsort
numpy
pandas
paramiko
parasail
pytest
python-circos
python-Levenshtein
pyyaml
sample-sheet
scikit-learn
scipy
seaborn
smart_open

All of the above dependencies can be installed with pip, and will be installed automatically when installing abutils with pip.

abutils packages several additional external binaries that are required for specific functions:

• abutils.tl.mafft uses MAFFT
• abutils.tl.muscle uses MUSCLE
• abutils.tl.cluster requires:
  • CD-HIT
  • MMseqs2
  • VSEARCH
• abutils.tl.fasttree requires FastTree

Althogh these binaries are all packaged into abutils, each respective abutils function provides the option to supply a different binary path in case you'd prefer to use a different version or an alternate compilation.