Skip to main content

Python Client library for PRIDE Rest API

Project description

pridepy: A Python package to download and search data from PRIDE database

Python package PyPI version PyPI - Downloads

Python Client library for PRIDE Rest API

Installation

From PyPI

To install, simply use pip:

$ pip install --upgrade pridepy

From Source

First, clone the repository on your local machine and then install the package using pip:

$ git clone https://github.com/PRIDE-Archive/pridepy
$ cd pridepy
$ pip install .

Install with setup.py:

$ git clone https://github.com/PRIDE-Archive/pridepy
$ cd pridepy
$ python setup.py sdist bdist_wheel 
$ pip install dist/pridepy-{version}.tar.gz

Examples

Download all the raw files from a dataset(eg: PXD012353). Warning: Raw files are generally large in size, so it may take some time to download depending on the number of files and file sizes.

-p: in download specifies protocol (ftp default):

  • ftp: FTP protocol
  • aspera: using the aspera protocol
  • globus: PRIDE globus endpoint (the data is downloaded through https)
$ pridepy download-all-public-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/ -p aspera

Download single file by name:

$ pridepy download-file-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt -p globus

NOTE: Currently we use Globus URLs (when -p globus is used) via HTTPS, not the Globus protocol. For more information about Globus, see Globus documentation.

Search projects with keywords and filters

$ pridepy search-projects-by-keywords-and-filters --keyword accession:PXD012353

Search files with filters

$ pridepy get-files-by-filter --filter fileCategory.value==RAW

Stream metadata of all projects as json and write it to a file

$ pridepy stream-projects-metadata -o all_pride_projects.json

Stream metadata of all files as json and write it to a file. Project accession can be specified as an optional parameter

$ pridepy stream-files-metadata -o all_pride_files.json
OR
$ pridepy stream-files-metadata -o PXD005011_files.json -a PXD005011

Use the below command to view a list of commands available:

$ pridepy --help
Usage: pridepy [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  download-all-public-raw-files   Download all public raw files...
  download-file-by-name           Download a single file from a...
  get-files-by-filter             get paged files :return:
  get-files-by-project-accession  get files by project accession...
  get-private-files               Get private files by project...
  get-projects                    get paged projects :return:
  get-projects-by-accession       get projects by accession... 
  stream-files-metadata           Stream all files metadata in...
  stream-projects-metadata        Stream all projects metadata...
    

NOTE

Please make sure you are using Python3, not Python 2.7 version.

White paper

A white paper is available at here. We can build it as PDF using pandoc.

$docker run --rm --platform linux/amd64 -v /Users/yperez/work/pridepy/paper/:/data -w /data openjournals/inara:latest paper.md -p -o pdf

Citation

Selvakumar Kamatchinathan, Suresh Hewapathirana, Chakradhar Bandla, Yasset Perez-Riverol. (2021, January 28). pridepy: A Python package to download and search data from PRIDE database (Version v0.0.3).

DOI

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pridepy-0.0.5.tar.gz (38.3 MB view hashes)

Uploaded Source

Built Distribution

pridepy-0.0.5-py3-none-any.whl (38.4 MB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page