gpha-ai-mutation-library

Library stores and updates tables for avian influenza mutations of interest.

Purpose

A utility that provides tables describing avian influenza mutations, in tsv format, for use in downstream applications.

There is a validation script that takes a new table(s), checks that the new data meets data requirements specified in the schema, and creates saves new tables, whilst moving the original table into an archive with an appropriate datestamp. This repository maintains three archived table sets.

Repo Layout

├── LICENSE
├── pyproject.toml
├── README.md
├── schemas
│   ├── ha_avian_influenza_mutation_table_gpha.yml
│   ├── m_avian_influenza_mutation_table_gpha.yml
│   ├── na_avian_influenza_mutation_table_gpha.yml
│   ├── np_avian_influenza_mutation_table_gpha.yml
│   ├── ns_avian_influenza_mutation_table_gpha.yml
│   ├── pa_avian_influenza_mutation_table_gpha.yml
│   ├── pb1_avian_influenza_mutation_table_gpha.yml
│   ├── pb2_avian_influenza_mutation_table_gpha.yml
│   └── reference_lists
│       ├── aa_list.txt
│       ├── feature_type_list.txt
│       ├── host_type_list.txt
│       ├── phenotypic_categories_list.txt
│       └── segment_list.txt
├── src
│   └── mutation_table_updater
│       ├── __init__.py
│       └── validate_and_update.py
├── tables
│   ├── ha_avian_influenza_mutation_table_gpha.tsv
│   ├── m_avian_influenza_mutation_table_gpha.tsv
│   ├── na_avian_influenza_mutation_table_gpha.tsv
│   ├── np_avian_influenza_mutation_table_gpha.tsv
│   ├── ns_avian_influenza_mutation_table_gpha.tsv
│   ├── pa_avian_influenza_mutation_table_gpha.tsv
│   ├── pb1_avian_influenza_mutation_table_gpha.tsv
│   └── pb2_avian_influenza_mutation_table_gpha.tsv
├── tests[...]
├── archive[...]
└── updates.log

[...] - Not shown for brevity

Usage

Accessing Tables

Tables should be read directly from GitHub with an appropriate URL i.e

wget https://github.com/ukhsa-collaboration/gpha-ai-mutation-library/tree/main/tables/

Updating Tables

The validation script will: - Updates logs - Take in either a table or folder containing tables. - Checks that the column headers are approriate - Checks expected data in columns meets requirements - If QC checks passed, archives original table(s) - Creates new table in main directory

Validate & update from a folder containing multiple tables

python \  
    src/mutation_table_updater/validate_and_update.py \  
    --input <TABLE_DIR>_avian_influenza_mutation_table.tsv \  
    --user <USERNAME>  

Validate & update a single file

python \  
    src/mutation_table_updater/validate_and_update.py \  
    --input <SEGMENT_ID>_avian_influenza_mutation_table.tsv \  
    --user <USERNAME>