pyproteome.pride package

This module provides functionality for accessing public data through PRIDE PRoteomics IDEntifications (PRIDE) / Proteome Xchange.

pyproteome.pride.fetch_data_set(accession, files=None)

Fetches files from a deposition on PRIDE.

Parameters:

accession : str

A PRIDE accession ID. i.e. ‘PXD001038’

files : dict of str, str

Download individual files to a specific location. By default, this function downloads all files to the current working directory.

Returns:

file_list : list of str

Files downloaded from a repository.

Examples

>>> pride.fetch_data_set(
...     'PXD001038',
...     files={'HJ070512_OCTFF_B2_All5Fractions_PeptideSummary.zip': '.'},
... )
['HJ070512_OCTFF_B2_All5Fractions_PeptideSummary.zip']

pyproteome.pride.list_data_set(accession)

Lists files contained in a deposition on PRIDE.

Information is fetched from pride.META_DATA_URL.

Parameters:

accession : str

Returns:

info_list : list of xml.etree.ElementTree

Information on files available in a repository.

Examples

>>> lst = pride.list_data_set('PXD003660')
>>> lst[0].get('name')
'20140524_MCF10A_E20VR1_ETP_TMT10.raw'
>>> lst[0].find('cvParam').get('value')
'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/06/PXD003660/20140524_MCF10A_E20VR1_ETP_TMT10.raw'