Evangelos Karatzas
Evangelos Karatzas
Agreed! A version pfamA_36.0.tar.gz would be awesome ;)
Thanks! I think it would make sense to rename the outputs to something like 1tim.pdb-A_0.fcz or 1tim.pdb_A_0.fcz, etc, in order to be able to split with a character and match...
Awesome!! Would be super cool to have such interface examples in your py-libraries documentation :D
Thanks! Looking forward to this. Running `esl-weight` at scale currently, is painfully slow...I am very curious to see if there will be a substantial execution time difference.
Well, we have a winner I guess. Definitely switching to pytrimmal :p Will test the new easel method and provide feedback though, hopefully within the next week. You are awesome.
I tried with `git+https://github.com/althonos/pyhmmer.git` but I get the error: `AttributeError: 'pyhmmer.easel.DigitalMSA' object has no attribute 'identity_filter'` :( Tried with both a conda env: https://github.com/EBI-Metagenomics/mgnifams/blob/switch-from-esl-weight/modules/local/generate_families/environment.yml and a Docker image (see recipe...
PyTrimal on the other hand works like a charm! Is there any plan to make it work with Stockholm alignments? Do you have any tool suggestions for reformatting MSAs between...
This was already extremely helpful, thanks ;)
And I guess neither can it work with pyhmmer DigitalMSA objects, correct? Even though I: ``` msa = msa.textize() pytrimal.Alignment(msa.names, [seq.sequence for seq in msa.sequences]) ```` I get this error:...
Is this being worked on or shall we close for now?