# 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
```
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
$docker run --rm --platform linux/amd64 -v /Users/yperez/work/pridepy/paper/:/data -w /data openjournals/inara:latest paper.md -p -o pdf
```
# Citation
Selvakumar Kamatchinathan, Suresh Hewapathirana, Chakradhar Bandla, Yasset Perez-Riverol. (2021, January 28). pridepy: A Python package to download and search data from PRIDE database (Version v0.0.3).
[](https://doi.org/10.5281/zenodo.4475414)
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"description": "# pridepy: A Python package to download and search data from PRIDE database\n\n[](https://github.com/PRIDE-Archive/pridepy/actions/workflows/python-package.yml)\n[](https://badge.fury.io/py/pridepy)\n\n\nPython Client library for PRIDE Rest API\n\n# Installation\n\n## From PyPI\n\nTo install, simply use `pip`:\n\n```bash\n$ 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\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# Citation\n\nSelvakumar 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). \n\n[](https://doi.org/10.5281/zenodo.4475414)\n",
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