Faster way to download PDBe PISA data
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Entering edit mode
7.4 years ago
Louis ▴ 150

I'm downloading PDBe PISA data as advised on the download page, via successive calls with lists of PDB codes such as http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?1kq1,4foj,3ga7,4err etc.

The download time seems to be varying (in the last few sets of 50 interfaces it's been between 3 and 5-6 minutes per set of IDs), so for the 2000+ queries it could take between 100 and 200 hours in total!

I'm wondering if it's common practice to parallelise this in some way (e.g. doing a download on one half somewhere else) or if anybody out there may have a full set that they could share?

I would have considered contacting PDBe but their site makes it pretty clear this is the recommended way to download the information.

P.S. the Python script I wrote for the task here allows for interrupted/resumed download if anyone reading this is seeking to do the same.

database Python • 2.6k views
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Entering edit mode
25 days ago
Wayne ▴ 510

I've got a more modernized and Pandas-integrated way to do this that I post about here. Snakemake allows you to just provide at a list of PDB identifiers for the script to process. The result will then be Pandas dataframes that can be integrated easily with downstream analysis.

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