# pridepy: A Python package to download and search data from PRIDE database
[](https://github.com/PRIDE-Archive/pridepy/actions/workflows/python-package.yml)
[](https://badge.fury.io/py/pridepy)
Python Client library for PRIDE Rest API
# Installation
## From PyPI
To install, simply use `pip`:
```bash
$ pip install --upgrade pridepy
```
## From Source
First, clone the repository on your local machine and then install the package using `pip`:
```bash
$ git clone https://github.com/PRIDE-Archive/pridepy
$ cd pridepy
$ pip install .
```
Install with setup.py:
```bash
$ 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_)
```bash
$ pridepy download-all-public-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/ -p aspera
```
Download single file by name:
```bash
$ 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](https://www.globus.org/data-transfer).
Search projects with keywords and filters
```bash
$ pridepy search-projects-by-keywords-and-filters --keyword accession:PXD012353
```
Search files with filters
```bash
$ pridepy get-files-by-filter --filter fileCategory.value==RAW
```
Stream metadata of all projects as json and write it to a file
```bash
$ 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
```bash
$ pridepy stream-files-metadata -o all_pride_files.json
OR
$ pridepy stream-files-metadata -o PXD005011_files.json -a PXD005011
```
This Python CLI tool, built using the Click module,
already provides detailed usage instructions for each command. To avoid redundancy and potential clutter in this README, you can access the usage instructions directly from the CLI
Use the below command to view a list of commands available:
```bash
$ 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](paper/paper.md). We can build it as PDF using pandoc.
```bash
$docker run --rm --platform linux/amd64 -v /Users/yperez/work/pridepy/paper/:/data -w /data openjournals/inara:latest paper.md -p -o pdf
```
# Contributing
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.
If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
1. Fork the Project
2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)
3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)
4. Push to the Branch (`git push origin feature/AmazingFeature`)
5. Open a Pull Request
# Citation
Selvakumar Kamatchinathan, Suresh Hewapathirana, Chakradhar Bandla, Juan Antonio Vizcaíno, Yasset Perez-Riverol. (2021, January 28). pridepy: A Python package to download and search data from PRIDE database (Version v0.0.3).
[](https://doi.org/10.5281/zenodo.4475414)
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"description": "# pridepy: A Python package to download and search data from PRIDE database\n\n[](https://github.com/PRIDE-Archive/pridepy/actions/workflows/python-package.yml)\n[](https://badge.fury.io/py/pridepy)\n\n\nPython Client library for PRIDE Rest API\n\n# Installation\n\n## From PyPI\n\nTo install, simply use `pip`:\n\n```bash\n$ pip install --upgrade pridepy\n```\n\n## From Source\n\nFirst, clone the repository on your local machine and then install the package using `pip`:\n\n```bash\n$ git clone https://github.com/PRIDE-Archive/pridepy\n$ cd pridepy\n$ pip install .\n```\n\nInstall with setup.py: \n\n```bash\n$ git clone https://github.com/PRIDE-Archive/pridepy\n$ cd pridepy\n$ python setup.py sdist bdist_wheel \n$ pip install dist/pridepy-{version}.tar.gz\n```\n\n# Examples\n\nDownload all the raw files from a dataset(eg: PXD012353).\nWarning: Raw files are generally large in size, so it may take some time to download depending on the number of files and file sizes.\n\n`-p`: in download specifies protocol (ftp default): \n - **ftp**: FTP protocol\n - **aspera**: using the aspera protocol\n - **globus**: PRIDE globus endpoint (_the data is downloaded through https_)\n\n```bash\n$ pridepy download-all-public-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/ -p aspera\n```\n\nDownload single file by name:\n```bash\n$ pridepy download-file-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt -p globus\n```\n\n>**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](https://www.globus.org/data-transfer).\n\nSearch projects with keywords and filters\n```bash\n$ pridepy search-projects-by-keywords-and-filters --keyword accession:PXD012353\n```\n\nSearch files with filters\n```bash\n$ pridepy get-files-by-filter --filter fileCategory.value==RAW\n```\n\nStream metadata of all projects as json and write it to a file\n```bash\n$ pridepy stream-projects-metadata -o all_pride_projects.json\n```\n\nStream metadata of all files as json and write it to a file. Project accession can be specified as an optional parameter\n```bash\n$ pridepy stream-files-metadata -o all_pride_files.json\nOR\n$ pridepy stream-files-metadata -o PXD005011_files.json -a PXD005011\n```\n\nThis Python CLI tool, built using the Click module, \nalready provides detailed usage instructions for each command. To avoid redundancy and potential clutter in this README, you can access the usage instructions directly from the CLI\nUse the below command to view a list of commands available:\n\n```bash\n$ pridepy --help\nUsage: pridepy [OPTIONS] COMMAND [ARGS]...\n\nOptions:\n --help Show this message and exit.\n\nCommands:\n download-all-public-raw-files Download all public raw files...\n download-file-by-name Download a single file from a...\n get-files-by-filter get paged files :return:\n get-files-by-project-accession get files by project accession...\n get-private-files Get private files by project...\n get-projects get paged projects :return:\n get-projects-by-accession get projects by accession... \n stream-files-metadata Stream all files metadata in...\n stream-projects-metadata Stream all projects metadata...\n \n```\n# NOTE\n\nPlease make sure you are using Python3, not Python 2.7 version.\n\n# White paper\n\nA white paper is available at [here](paper/paper.md). We can build it as PDF using pandoc.\n\n```bash\n$docker run --rm --platform linux/amd64 -v /Users/yperez/work/pridepy/paper/:/data -w /data openjournals/inara:latest paper.md -p -o pdf\n```\n\n# Contributing\n\nContributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated**.\n\nIf you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag \"enhancement\".\n\n1. Fork the Project\n2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)\n3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)\n4. Push to the Branch (`git push origin feature/AmazingFeature`)\n5. Open a Pull Request\n\n# Citation\n\nSelvakumar Kamatchinathan, Suresh Hewapathirana, Chakradhar Bandla, Juan Antonio Vizca\u00edno, Yasset Perez-Riverol. (2021, January 28). pridepy: A Python package to download and search data from PRIDE database (Version v0.0.3). \n\n[](https://doi.org/10.5281/zenodo.4475414)\n",
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