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https://github.com/wfondrie/ppx

A Python interface to proteomics data repositories
https://github.com/wfondrie/ppx

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A Python interface to proteomics data repositories

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# A Python interface to proteomics data repositories



[![conda](https://img.shields.io/conda/vn/bioconda/ppx?color=green)](http://bioconda.github.io/recipes/ppx/README.html)

[![PyPI](https://img.shields.io/pypi/v/ppx?color=green)](https://pypi.org/project/ppx/)

[![tests](https://github.com/wfondrie/ppx/actions/workflows/tests.yml/badge.svg?branch=master)](https://github.com/wfondrie/ppx/actions/workflows/tests.yml)

[![Documentation Status](https://readthedocs.org/projects/ppx/badge/?version=latest)](https://ppx.readthedocs.io/en/latest/?badge=latest)



https://github.com/wfondrie/ppx/workflows/tests/badge.svg?branch=master



## Overview

ppx provides a simple, programmatic means to access proteomics data that are

publicly available in [ProteomeXchange](http://www.proteomexchange.org) partner

repositories. ppx allows users to easily find and download files associated

with projects in [PRIDE](https://www.ebi.ac.uk/pride/archive/) and

[MassIVE](https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp). In doing so,

ppx promotes the reproducible analysis of proteomics data.



For full documentation and examples, visit: https://ppx.readthedocs.io



## Installation

ppx requires Python 3.6+ and depends upon the

[requests](https://docs.python-requests.org/en/master/) and

[tqdm](https://tqdm.github.io/) Python packages. ppx and any missing

dependencies are easily installed with `pip` or with `conda` through the

[bioconda](https://bioconda.github.io/index.html) channel.



Install with `conda`:



``` shell

conda install -c bioconda ppx

```



Or install with `pip`:



```shell

pip3 install ppx

```



## Configuration



By default, ppx will download project files in the `.ppx` directory under the

current user's home directory (`~/.ppx` on Linux and MacOS). There are several

ways to specify different data directories:



1. Change the ppx data directory for all future Python sessions by setting the

`PPX_DATA_DIR` environment variable to your preferred directory.



2. Change the ppx data directory for a Python session using the

`ppx.set_data_dir()` function.



3. Specify a data directory for a project using the `local` argument:



``` Python

>>> import ppx



>>> proj = ppx.find_project("PXD000001", local="my/data/dir")

```



Why does ppx set a default data directory? We found that this makes it easier

to reuse the same proteomics data files in multiple tasks that we're working

on.



As of ppx v1.3.0, cloud paths can also be used as the data directory. This

allows you to stream downloaded files to AWS S3, Google Cloud Storage, or Azure

Blob Storage. To use a cloud storage provider, simply set the data directory to

a cloud URI, such as :code:`s3://my-data-bucket/ppx` using any of the methods

above. Please note that you'll also need to setup credentials for your cloud

provider---see the `CloudPathLib documentation

_` for details.



## Examples

First, find a project using its ProteomeXchange or MassIVE identifier:



``` Python

>>> import ppx



>>> proj = ppx.find_project("PXD000001")

```



We can then view the files associated with the project in the repository

(PRIDE in this case):



``` Python

>>> proj.remote_files()

#['F063721.dat',

# 'F063721.dat-mztab.txt',

# 'PRIDE_Exp_Complete_Ac_22134.xml.gz',

# 'PRIDE_Exp_mzData_Ac_22134.xml.gz',

# 'PXD000001_mztab.txt',

# 'README.txt',

# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML',

# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzXML',

# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzXML',

# 'TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.raw',

# 'erwinia_carotovora.fasta',

# 'generated/PRIDE_Exp_Complete_Ac_22134.pride.mgf.gz',

# 'generated/PRIDE_Exp_Complete_Ac_22134.pride.mztab.gz']

```



We can also [glob](https://en.wikipedia.org/wiki/Glob_(programming)) for

specific types of files:



``` Python

>>> proj.remote_files("*.mzML")

# ['TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML']

```



Then we can download one or more files to the projects local data directory:



``` Python

>>> proj.download("README.txt")

# [PosixPath('/Users/wfondrie/.ppx/PXD000001/README.txt')]

```



Once we've downloaded files, ppx no longer needs an internet connection to

retrieve a project's local data. However, you will need to specify the

repository in which the project data resides. If we start a new Python

session, we can find our previous file easily:



``` Python

>>> import ppx



>>> proj = ppx.find_project("PXD000001", repo="PRIDE")

>>> proj.local_files()

# [PosixPath('/Users/wfondrie/.ppx/PXD000001/README.txt')]

```



### Downloading to cloud storage backend



We use [CloudPathlib](https://cloudpathlib.drivendata.org/stable/) to power

support for AWS S3, Google Cloud Storage, and Azure Blob Storage. To use a

cloud storage provider, create the bucket for ppx to use and set it as the ppx data

directory.



For example using AWS S3, we can save the files of a project to an S3 bucket:

``` python

>>> proj = ppx.find_project("PXD000001", local="s3://my-bucket/PXD000001")

>>> proj.download("README.txt")

# [S3Path('s3://my-bucket/PXD000001/README.txt')]

```



CloudPathLib then provides methods to download files from S3 when you need them:



``` Python

>>> readme_on_s3 = proj.local_files("README.txt")[0]

>>> readme_on_s3.download_to("README.txt")

# [PosixPath(README.txt)]

```



## If you are an R user...



ppx was inspired the rpx R package by Laurent Gatto. Check it out on

[Bioconductor](http://bioconductor.org/packages/release/bioc/html/rpx.html) and

[GitHub](https://github.com/lgatto/rpx).