Python Client library for PRIDE Rest API
Project description
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).
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