SIFTS

[t9lex]

I have been downloading the SIFTS dataset for two days now in order to calculate the contact matrix through multiple sequence alignment. How long does it usually take to download this dataset?

[thomashopf]

It can take quite a while to download this (on the order of hours), as lots of sequences need to be downloaded using the UniProt API.

Is this using the latest code from the develop branch?

[t9lex]

I understand that you are able to download the CSV file, but encountering an error when trying to download the FA file. I apologize for any confusion earlier.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/luoqichao/Liyingcan/evcouplings/EVcouplings-develop/databases/sifts/shuju.py", line 13, in
s = SIFTS("../../databases/sifts/pdb_chain_uniprot_plus.csv", "../../databases/sifts/pdb_chain_uniprot_plus.fa")
File "/home/luoqichao/miniconda3/lib/python3.9/site-packages/evcouplings/compare/sifts.py", line 355, in init
self.create_sequence_file(sequence_file)
File "/home/luoqichao/miniconda3/lib/python3.9/site-packages/evcouplings/compare/sifts.py", line 539, in create_sequence_file
raise ResourceError(
evcouplings.utils.system.ResourceError: Could not fetch sequences for SIFTS mapping tables from UniProt since maximum number of retries after connection errors was exceeded. Retry at a later time, or call SIFTS.create_sequence_file() with a higher value for max_retries.

[t9lex]

Yesterday I used the nohup command to download fast data, and it started downloading but stopped at 30M and didn't proceed further.

[t9lex]

I saw a comment saying that fasta data can also be directly downloaded from somewhere. Can you please provide me with the website? I would like to try this method.