pyhmmer

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[question] PyInfernal?

3

Hi Martin, Many thanks for all your work on Python-izing useful tools! 😄 I wondered if there was a plan to build Cython bindings and Python interface to [infernal](https://github.com/EddyRivasLab/infernal)? Cheers,...

tomdstanton

Possibility to filter alignment results on coverage between HMM and target

6

Hi ! I was searching if that's possible to report the alignment coverage on the HMM and the target. I'm using the [PADLOC-DB](https://github.com/padlocbio/padloc-db) as HMM database and I notice that...

jpjarnoux

Apply cutoffs for domains

3

This is more of a question than a bug. My understanding is that when the user set a cutoff, PyHMMER will not report hits that would have `hit.included == False`....

apcamargo

Hi Martin, I'm trying to align multiple HMM to proteins; some of my HMM has a GA score, and others do not. Is there a way to leave hmmsearch to...

jpjarnoux

[Feature Request] Internally assigning Z for ```HMM``` class

3

Hello! Thank you for the awesome and much-needed package. I wanted to ask if there could be an internal way to determine the Z value or if it can be...

erfanshekarriz

cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```

1

Hello and hope all is well. I'm running into issues reproducing this code (https://pyhmmer.readthedocs.io/en/stable/examples/performance_tips.html#Search-and-scan): ```python import time import pyhmmer t1 = time.time() with pyhmmer.plan7.HMMFile("data/hmms/bin/t2pks.h3m") as hmms: with pyhmmer.easel.SequenceFile("data/seqs/938293.PRJEB85.HG003687.faa", digital=True) as...

erfanshekarriz

Use hpc_hmmsearch

6

This might be outside of the scope of the project, but I thought it could be a nice addition. There's a modified version of hmmseach (https://github.com/Larofeticus/hpc_hmmsearch) that runs *way* faster...

apcamargo

Production stable or WIP

1

Hi Martin, thanks a lot for this wonderful Python bindings project (and all others). We're keen to use this to replace HMMER in [Bakta](https://github.com/oschwengers/bakta/pull/219) and we're quite happy with the...

oschwengers

Conflict with numba

2

I wrote a package to run the Viterbi hmm-profile alignment algorithm on hmmer3 profiles. The package uses pyhmmer to parse the hmm files and get numpy arrays from the values....

seanrjohnson

zip argument #1 must support iteration error + other question

1

Hey Martin, Thanks for making this tool, I'm finding it very useful for my current project. I have a profile hmm database obtained from CONJScan that I want to use...

willhuynh11