search

LysSanzMoreta / LYS_Automatic_Search

Other
0 stars 1 forks source link

getBlastPDB api shutdown #1

Open altingia opened 6 days ago

altingia commented 6 days ago

LYS_PDB_Search.py line93: url = "http://www.rcsb.org/pdb/rest/getBlastPDB1?sequence=%s&eCutOff=1e-6&matrix=BLOSUM62" % (gene_sequence)

the getBlastPBD, Legacy API Shutdown, how to update with the new api?

LysSanzMoreta commented 6 days ago

Yeah, I would have to look into that, they have made quite some changes.

They announced the shutdown here: https://www.rcsb.org/news/5fc9176809ae2a096d081e28

I am afraid you will have to find a work around on your own for the moment. I do not have much time for this at the moment. If I get to update these scripts I would have to re-do them entirely because they require quite some improvement.

I am pretty sure there are some methods out there to Blast again the PDB database and retrieve the homolog structure. Once you manage to retrieve the sequences, the rest of the script should work though (perhaps some small pandas error or so).