Pypath inputs status report

Here we take a snapshot from the current tip of the master branch of pypath, collect all functions from the pypath.inputs module and run them with an empty cache directory. Basic metrics about the returned values and errors are presented. This simple and automatized procedure is able to reveal the most common errors: if a server is down, if the URL, format or access restrictions changed, or pypath got broken in the recent developments. Note: this report is only about pypath, not about the data in the OmniPath web service; before we build the OmniPath database, we aim to fix the errors which could have an impact on its content.

Compiled between 2021-09-03 22:11:13 and 2021-09-03 22:11:23; pypath version: 0.12.0 (from git; 7190eee )

Modules tested: 2
Functions tested: 3
Functions run without error: 3
Functions skipped due to lack of arguments: 0
Functions run with error: 0

Function Started Finished Elapsed (s) Result type Result repr Result size Error
pypath.inputs.abs.abs_interactions 2021-09-03 22:11:18 2021-09-03 22:11:19 1.0 list [['SRF', 'extracted04'], ['SRF', 'extracted04'], ['SRF', 'extracted04'], ['TEF1', 'extracted04'], ['SP1', 'extracted04'], ['TBP', 'extracted04'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['SRF', 'X67686'], ['TEF1', 'X67686'], ['SP1', 'X67686'], ['TBP', 'X67686'], ['SRF', 'extracted05'], ['SRF', 'extrac...(truncated) 650
pypath.inputs.acsn.acsn_interactions 2021-09-03 22:11:19 2021-09-03 22:11:20 1.0 list [AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CA', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454;15509806;16288288;17646672;18644865;20673124'), AcsnInteraction(partner_a='FOXO3', partner_b='PIK3CB', mechanism='CATALYSIS', references='10783894;11094066;11154281;11994454...(truncated) 37,725
pypath.inputs.acsn.acsn_interactions_sif 2021-09-03 22:11:20 2021-09-03 22:11:20 0.0 list [['ACHE', 'UNKNOWN_CATALYSIS', 'Cytochrome'], ['ACHE', 'UNKNOWN_CATALYSIS', 'APAF1'], ['E2F1', 'null', 'MIR17-3P'], ['E2F1', 'null', 'p14ARF'], ['E2F1', 'null', 'BAF250'], ['E2F1', 'null', 'HDAC1'], ['E2F1', 'null', 'HP1gamma'], ['E2F1', 'null', 'RB1'], ['E2F1', 'null', 'SUV39H1'], ['E2F1', 'null', ...(truncated) 9,570

The OmniPath Team Saez Lab 2021-09-03