How to automatically create a PEP from GEO or SRA

geofetch is a command-line utility that converts GEO or SRA accessions into PEP projects. You provide an accession (or a spreadsheet with a list of accessions), and geofetch with produce the PEP (both project config and sample annotation). geofetch can also download the data from SRA, so your project will be ready for direct input into any PEP-compatible tool.

Code and documentation

Quick start

geofetch is a python package that can be installed from PyPI:

pip install geofetch

To see the command-line options, run it with -h:

geofetch --help

For example, you can run geofetch to build a PEP for a GSE accession like this:

geofetch -i GSE##### -m path/to/metadata/folder -n PROJECT_NAME