PEP compatible Run pytests docs-badge pypi-badge Code style: black

geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA. When given one or more GEO/SRA accessions, geofetch will:

  • Download either raw or processed data from either SRA or GEO
  • Produce a standardized PEP sample table. This makes it really easy to run looper-compatible pipelines on public datasets by handling data acquisition and metadata formatting and standardization for you.
  • Prepare a project to run with sraconvert to convert SRA files into FASTQ files.

Quick example

geofetch runs on the command line. This command will download the raw data and metadata for the given GSE number.

geofetch -i GSE95654

You can add --processed if you want to download processed files from the given experiment.

geofetch -i GSE95654 --processed

You can add --just-metadata if you want to download metadata without the raw SRA files or processed GEO files.

geofetch -i GSE95654 --just-metadata
geofetch -i GSE95654 --processed --just-metadata

For more details, check out the usage reference, installation instructions, or head on over to the tutorial for raw data and tutorial for processed data for a detailed walkthrough.