Rfam Production Code

About

This repository provides a set of tools related to the Rfam production pipeline. The collection includes script for data export, database processing, visualization and validation.

Scripts

Export: Data Export tools
Processing: Database processing tools
View: Rfam family view process related scripts
Validation: Data validation scripts
Utils: Support modules/utilities

Using with Docker

build container
```
docker build -t rfam-production .
```

open bash interactive shell

docker run -v `pwd`:/rfam/rfam-production -it rfam-production bash

run a command inside the container

docker run -v `pwd`:/rfam/rfam-production -it rfam-production python scripts/export/rfam_xml_dumper.py --out /rfam --type C

Installation

# install Python dependencies
pip install -r requirements.txt

# set up Python path
export PYTHONPATH=/path/to/the/project

# create and edit configuration file (excluded from version control)
cp config/rfam_local_template.py config/rfam_local.py

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