PRIDE projects

class ppx.PrideProject(pride_id, local=None, fetch=False, timeout=10.0)[source]

Retrieve information about a PRIDE project.

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

Parameters:

pride_idstr: The PRIDE 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.
fetchbool, optional: Should ppx check the remote repository for updated metadata?
timeoutfloat, optional: The maximum amount of time to wait for a server response.

Attributes:

idstr: The repository identifier.
localPath object: The local data directory for this project.
urlstr: The FTP address associated with this project.
titlestr: The title of this project.
descriptionstr: A description of this project.
doistr: The DOI for this project.
data_processing_protocolstr: The data processing protocol for this project.
sample_processing_protocolstr: The sample processing protocol for this project.
metadatadict: The project metadata as a nested dictionary.
fetchbool: Should ppx check the remote repository for updated metadata?
timeoutfloat: The maximum amount of time to wait for a server response.

Methods

`download`(files[, force_, silent])	Download files from the remote repository.
`local_dirs`([glob])	List the local directories associated with this project.
`local_files`([glob])	List the local files associated with this project.
`remote_dirs`([glob])	List the project directories in the remote repository.
`remote_files`([glob])	List the project files in the remote repository.

property url: The FTP address associated with this project.

property metadata: The project metadata as a nested dictionary.

property title: The title of this project.

property description: A description of this project.

property sample_processing_protocol: The sample processing protocol for this project.

property data_processing_protocol: The data processing protocol for this project.

property doi: The DOI for this project.

download(files, force_=False, silent=False)

Download files from the remote repository.

These files are downloaded to this project’s local data directory (local). By default, ppx will not redownload files with matching file names already present in the local data directory.

Parameters:

filesstr or list of str: One or more files to be downloaded from the remote repository.
force_bool, optional: Force the files to be downloaded, even if they already exist.
silentbool, optional: Hide download progress bars?

Returns:

list of Path objects: The paths of the downloaded files.

property fetch: Should ppx check the remote repository for updated metadata?

property id: The repository identifier.

property local: The local data directory for this project.

local_dirs(glob=None)

List the local directories associated with this project.

Parameters:

globstr, optional: Use Unix wildcards to return specific files. For example, "*peak" would return all directories ending in “peak”.

Returns:

list of str: The local directories available for this project.

local_files(glob=None)

List the local files associated with this project.

Parameters:

globstr, optional: Use Unix wildcards to return specific files. For example, "*.mzML" would return all of the mzML files.

Returns:

list of str: The local files available for this project.

remote_dirs(glob=None)

List the project directories in the remote repository.

Parameters:

globstr, optional: Use Unix wildcards to return specific files. For example, "*peak" would return all directories ending in “peak”.

Returns:

list of str: The remote directories available for this project.

remote_files(glob=None)

List the project files in the remote repository.

Parameters:

globstr, optional: Use Unix wildcards to return specific files. For example, "*.mzML" would return all of the mzML files.

Returns:

list of str: The remote files available for this project.

property timeout: The maximum amount of time to wait for a server response.