Functions

ppx.find_project(identifier, local=None, repo=None, fetch=False, timeout=10.0)[source]

Find a project in the PRIDE or MassIVE repositories.

Parameters:
identifierstr

The project identifier.

localstr, pathlib.Path, or cloudpathlib.CloudPath, optional

The local data directory in which the project files will be downloaded. In addition to local paths, paths to AWS S3, Google Cloud Storage, or Azure Blob Storage can be used. The default is ~/.ppx

repo{“pride”, “massive”}, optional

The repository in which to look for the project. If None, ppx will try to figure it out.

fetchbool, optional

Should ppx check the remote repository for updated metadata?

timeoutfloat, optional

The maximum amount of time to wait for a server response

Returns:
PrideProject or MassiveProject

An object to interact with the project data in the repository.

ppx.get_data_dir()[source]

Retrieve the current data directory for ppx.

ppx.set_data_dir(path=None)[source]

Set the ppx data directory.

Parameters:
pathstr or pathlib.Path object, optional

The path for ppx to use as its data directory.

ppx.pride.list_projects(timeout=10.0)[source]

List all available projects on PRIDE

PRIDE Archive: https://www.ebi.ac.uk/pride/archive/

Parameters:
timeoutfloat, optional

The maximum amount of time to wait for a response from the server.

Returns:
list of str

A list of PRIDE identifiers.

ppx.massive.list_projects(timeout=10.0)[source]

List all available projects on MassIVE.

MassIVE: https://massive.ucsd.edu

Parameters:
timeoutfloat, optional

The maximum amount of time to wait for a response from the server.

Returns:
list of str

A list of MassIVE identifiers.