hlagenie 0.0.2

Sequence handing for HLA with Python

HLAgenie

Python package for dealing with HLA sequence data

Quick-Start Guide

Installation

Install from PyPI

pip install HLAgenie

Install from source

python3 -m venv venv
source venv/bin/activate
python setup.py install

Available loci:

1. A
2. B
3. C
4. DPA1
5. DPB1
6. DQA1
7. DQB1
8. DRB1

Supported functions

Initialize the HLAGenie object

Instantiate the object with the IPD-IMGT/HLA database version. This will create a SQLite database of sequences in the /tmp directory.

import hlagenie

genie = hlagenie.init("3510")

Retrieve amino acid position from mature protein sequence

Get the amino acid residue at a given position in a given allele's mature protein sequence. This is 1-indexed, not 0-indexed.

genie.getAAposition("A*01:01",1)

TODO

• Add documentation for other functions
• Add example output