kblin / rna_extract

Extract tRNAs and rRNAs from sequences identified by NCBI GenBank ID

Extract RNA features from sequences identified by NCBI GenBank ID

Shaun (@sjackman) was asking for a script to download tRNAs and rRNAs for a sequence identified by NCBI GenBank ID.

While this violates the requirements of "curl to Entrez or E-utilities" as only dependency, I just wanted to show how easy this task is with a bit of Python.

Installation

git clone https://github.com/kblin/rna_extract.git && cd rna_extract
# recommended: create/activate a python virtualenv here (using virtualenv or conda)
pip install -r requirements.txt

Usage

./rna_extract.py NC_003888 > my_rnas.fa

You can use the --reuse flag to skip donloading GenBank files that already exist in your current directory.

License

This script is licensed under the Apache 2 license. See LICENSE for details.