Utilities for analysis of adaptive immune receptor repertoire (AIRR) data
Project description
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 MAFFTabutils.tl.muscle
uses MUSCLEabutils.tl.cluster
requires: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.
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