prody
Pfam not completely working
For example, the AMPAR test only gives 2 out of 4 pfam domains at least sometimes
@atbogetti, any chance you could check this too please seeing as you’ve just been over the pfam code changes?
@jamesmkrieger Yes, I have actually started to look into this already. I will figure it out.
@jamesmkrieger I tried the pfam tests and also encountered failures. I have narrowed down the source of the issue to this line: https://github.com/prody/ProDy/blob/412c8fa9b18f78065bea4d9a641f77a520dc0892/prody/database/pfam.py#L421-L422. For some reason, that way of selecting the residues is causing the following error: TypeError: can't multiply sequence by non-int of type 'Forward'. I tried manually inputting the range and got the same error, though when I just use a single number as the selection (for instance, resindex 10) it works just fine. Do you know if something changed in the residue selection language recently? I can dig deeper but just wanted to see if this may be familiar to you before proceeding.
I don’t think it changed. The selection parser is too complicated to change really. Maybe something changed in pyparsing though
Bingo. I downgraded pyparsing to v3.1.1 (current is 3.1.2) and it works now. The pfam tests also all pass without any failures.
Can you revert #1816 and see if they still pass please?
Also, please can you check if this fixes the problems with the latest numpy versions too (see #1655)?
Bingo. I downgraded pyparsing to v3.1.1 (current is 3.1.2) and it works now. The pfam tests also all pass without any failures.
Actually, that's not true. The pfam tests pass because I changed them. The original tests still fail if we change the pyparsing version (see https://github.com/prody/ProDy/actions/runs/8294288857?pr=1845), so I don't think that's actually the issue here although it's definitely an issue that we have to fix (see also #1844).
Can you revert #1816 and see if they still pass please?
This was the wrong number. The one I meant was #1825, which I have reverted in #1845 that led to the tests failing as mentioned above. Sorry
Also, please can you check if this fixes the problems with the latest numpy versions too (see #1655)?
The numpy thing with pyparsing is now checked and that indeed fixed it.