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
geofetch is a python package that can be installed from PyPI:
pip install geofetch
To see the command-line options, run it with
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