Automatically download samples from ENA and process them through the Molgenis Compute pipeline for RNAseq genotyping.
Needs Python 3 (tested with 3.5.2)
To install, do
python setup.py install
To run all unittests, do
python setup.py test
# BELOW IS OUT OF DATE To download the current RNA-seq samplesheet to your /tmp directory
import genotypePublicData # Get the Homo Sapien samples (tax 9606). Change for samples of different organism tax = '9606' # Get the RNA-seq samples library_strategy = 'RNA-seq' download_ena_samples = genotypePublicData.Download_ENA_samplesheet(tax, library_strategy) download_ena_samples.download_samplesheet('/tmp')