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

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).