hgmd merge_expand data generation - Githubissues

LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis

GNU General Public License v3.0

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hgmd merge_expand data generation #100

Closed SpicyChicken6 closed 2 weeks ago

SpicyChicken6 commented 2 weeks ago

Files to update

This PR provides scripts to generate the 4 files as shown in merge_expand folder

What's in this PR

A simple amino acid table: AA_abbreviations.txt
A setup script that prepares the environment for running expandvar.R: setup.sh
The reorganized script with rewritten functions for speed (originally from Dongxue): expandvar.R

Testing

[x] hg19
- 2024 version of hgmd transvar results retains 91.3% of annotations from 2022 version, plus more variants in 2024 version
[x] hg38
- 2024 version of hgmd transvar results retains 84% of annotations from 2022 version, plus more variants in 2024 version

Notes

The script took about 1 hour 40 minutes to run. The speed limiting step here is running Transvar program.