Metadata-Version: 2.1
Name: geofetch
Version: 0.11.1
Summary: Downloads data and metadata from GEO and SRA and creates standard PEPs.
Home-page: https://github.com/pepkit/geofetch/
Author: Oleksandr Khoroshevskyi, Nathan Sheffield, Vince Reuter, Nathan LeRoy
License: BSD2
Keywords: project,bioinformatics,sequencing,ngs,workflow,GUI
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: attmap (>=0.1.8)
Requires-Dist: colorama (>=0.3.9)
Requires-Dist: logmuse (>=0.2.6)
Requires-Dist: ubiquerg (>=0.6.2)
Requires-Dist: requests (>=2.28.1)
Requires-Dist: xmltodict (>=0.13.0)
Requires-Dist: pandas (>=1.3.5)
Requires-Dist: peppy (>=0.35.1)
Requires-Dist: rich (>=12.5.1)
Requires-Dist: coloredlogs (>=15.0.1)

# <img src="https://raw.githubusercontent.com/pepkit/geofetch/master/docs/img/geofetch_logo.svg?sanitize=true" alt="geofetch logo" height="70">

[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pepkit.github.io)
![Run pytests](https://github.com/pepkit/geofetch/workflows/Run%20pytests/badge.svg)
[![docs-badge](https://readthedocs.org/projects/geofetch/badge/?version=latest)](https://geofetch.databio.org/en/latest/)
[![pypi-badge](https://img.shields.io/pypi/v/geofetch)](https://pypi.org/project/geofetch)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

`geofetch` is a command-line tool that downloads sequencing data and metadata from GEO and SRA and creates [standard PEPs](https://pep.databio.org/). `geofetch` is hosted at [pypi](https://pypi.org/project/geofetch/). You can convert the result of geofetch into unmapped `bam` or `fastq` files with the included `sraconvert` command.

Key geofetch features:

- Works with GEO and SRA metadata
- Combines samples from different projects
- Standardizes output metadata
- Filters type and size of processed files (from GEO) before downloading them
- Easy to use
- Fast execution time
- Can search GEO to find relevant data
- Can be used either as a command-line tool or from within Python using an API

For more information, see [complete documentation at geofetch.databio.org](http://geofetch.databio.org) (source in the [/docs](/docs) folder).
