I have a fresh version of omxware lib from today, loaded in Jupyter Notebook. Token is accepted, help(omx) prints expected text.
I run this example taken straight from the COVID-19 Quick Start Notebook:
search_term = ‘Replicase polyprotein 1a’
proteins = omx.proteins(protein_name=search_term,page_size=25,classification=‘virus’,collection = [‘sars-cov-2’])
total = proteins.total_results()
… and get 0 results.
No error, just 0 results.
What I really need are unique protein sequences for all SARS-COV-2 variants, i.e. 1198 sequences.
I tried retrieving proteins from the COVID-19 collection using ids=all and that returned a ridiculous 55M records.
I now get 0 results for everything I run, so I assume I have been blocked in some way or blacklisted because the examples should work… or has the API changed?
I came here in desperation after realizing that ViPR is only returning a fraction of available protein sequences. I have people waiting in the lab for data that relies on those sequences.
Any help greatly appreciated.