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 two components of a PEP: the project config file and the sample annotation file.
geofetch will also download the data from SRA, so your project will be ready for direct input into any PEP-compatible tool.
Code and documentation
- User documentation and vignettes pending
- Source code at Github
geofetch is a python script that can be downloaded from github:
git clone firstname.lastname@example.org:pepkit/geofetch.git
To see the command-line options, run it with
python geofetch.py -h
For example, you can run
geofetch to build a PEP for your list of accessions like this:
python geofetch.py -i GSE##### -m path/to/metadata/folder -n PROJECT_NAME