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).
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
Built Distribution
File details
Details for the file pridepy-0.0.5.tar.gz
.
File metadata
- Download URL: pridepy-0.0.5.tar.gz
- Upload date:
- Size: 38.3 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.9.20
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 548b4a848ffe7bef7e0dd7b15a4c844d0db1cf30563ae5ff5e484313b0a9441d |
|
MD5 | 687d1265ebca8c5f871733b0814341e7 |
|
BLAKE2b-256 | c6692f94d70cf30d3f20ea21107e6fb3b709b9236407224f3e6f066844b5cc27 |
File details
Details for the file pridepy-0.0.5-py3-none-any.whl
.
File metadata
- Download URL: pridepy-0.0.5-py3-none-any.whl
- Upload date:
- Size: 38.4 MB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/5.1.1 CPython/3.9.20
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | ba91aef7a55b90c6361a62b3f751ec80187a4c46bd090793b020a847edb60ae4 |
|
MD5 | 48a80f0da4d876cc37638aa689c91082 |
|
BLAKE2b-256 | 479628f1e1f24272d1134cd2b4b88a1641d41013cdc973f7362cfe2f90a02a9c |