Sequence handing for HLA with Python
Project description
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:
- A
- B
- C
- DPA1
- DPB1
- DQA1
- DQB1
- 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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
hlagenie-0.0.2.tar.gz
(22.4 kB
view hashes)
Built Distribution
Close
Hashes for hlagenie-0.0.2-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 34df553e845e54f51dcdd2c23e5458dcda8e8c60ee93c213aa96eecaae1530c5 |
|
MD5 | 170e09e812f343e64d38deb5e0186d1c |
|
BLAKE2b-256 | 762754dfcf7f138db3893876c9f0427e925575bdc3abc3531d708462e67eea01 |