geofetch

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

Quick start

geofetch is a python script that can be downloaded from github:

git clone git@github.com:pepkit/geofetch.git

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

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


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