https://github.com/jhrcook/protein-language-models

Experimenting with protein language model predictions
https://github.com/jhrcook/protein-language-models

data-analysis protein-language-model variant-effect-prediction

Last synced: 7 days ago
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Experimenting with protein language model predictions

• Host: GitHub
• URL: https://github.com/jhrcook/protein-language-models
• Owner: jhrcook
• Created: 2023-10-16T22:06:24.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2023-10-16T22:08:36.000Z (over 1 year ago)
• Last Synced: 2024-11-13T22:44:33.590Z (2 months ago)
• Topics: data-analysis, protein-language-model, variant-effect-prediction
• Language: Python
• Homepage:
• Size: 3.91 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Protein language models

## Setup

```bash

pyenv local 3.11

python -m venv .env

source .env/bin/activate

pip install --upgrade pip

pip install -r requirements.txt

```

```bash

pre-commit install

```

## Data preparation

Run the following script to download and prepare the raw data:

```bash

./prepare_data.py

```

Data sources:

downloaded AlphaMissesnse predictions: 

downloaded the file: "AlphaMissense_aa_substitutions.tsv.gz"

ESM1b paper: 

Downloaded ESM1b: 

downloaded the file: "ALL_hum_isoforms_ESM1b_LLR.zip"

Copied them to "raw-data/"