This repository contains a collection of modules for RNA-seq analyses:
annotation: module for representing and working with gene annotations in GTF format.rnaseqnorm: collection of functions for RNA-seq normalization, including DESeq size factors (Anders & Huber, 2010) and TMM (Robinson & Oshlack, 2010).
Clone this repository:
git clone git@github.com:francois-a/rnaseq-utils.git
Add the repository to your Python path:
export PYTHONPATH=$PYTHONPATH:/<path_to>/rnaseq-utils
Download the GENCODE 30 GTF:
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz
Load annotation
import annotation
annot = annotation.Annotation('gencode.v30.annotation.gtf.gz')
Get gene by HGNC symbol:
gene = annot.get_gene('MYL9')
Display information:
print(gene)