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KosinskiLab / AlphaPulldown

https://doi.org/10.1093/bioinformatics/btac749
GNU General Public License v3.0
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pi-score outputs #329

Closed salomonssonj closed 1 month ago

salomonssonj commented 2 months ago

Hi,

In the previous version of AlphaPulldown we obtained a folder with outputs from pi-score, such as interface residues and interface chain contacts. Is it possible to get these files for AP2.0 as well? We find them quite useful when evaluating the predications.

Kindly, Johannes

dingquanyu commented 2 months ago

Hi Johannes,

Sorry in the new version I moved this step to be done within a temporary directory, which will remove the intermediate files after the calculations. You still can find these parameters in the final csv table.

Yours Dingquan

jkosinski commented 2 months ago

Hmm, I think Johannes means lists of "interface residues and interface chain contacts", which are not in the table. If that info is there, I think we should keep those folders indeed!

salomonssonj commented 2 months ago

Hi Dingquan and Jan,

Yes, exactly. It’s the lists of this information that I miss, which currently are not included in the .csv file.

Thanks.

dingquanyu commented 2 months ago

I see. I will change it so it keeps the output folder.

salomonssonj commented 2 months ago

Great, much appreciated. Thank you!

DimaMolod commented 2 months ago

@maurerv then we need to revert back snakemake file. Can we move the files only if they are available so that it doesn't lead to crash?

dingquanyu commented 2 months ago

@maurerv then we need to revert back snakemake file. Can we move the files only if they are available so that it doesn't lead to crash?

@DimaMolod maybe it's better that you create an issue in the snakemake repo and refers to this issue, otherwise this one will be closed once the #330 PR is merged and you may lose the track