Comments (1)
althonos
commented on August 25, 2024
1
Hi Kamil, thanks for the bug report!
I traced back the bug in the Offsets class, causing file offsets not to be recorded properly in pyhmmer.hmmer.hmmpress, causing errors later when trying to load the pressed HMMs. I made a patch which will be released with the upcoming v0.8.0.
In the meantime, if you really want to press your HMMs you can use the actual hmmpress from HMMER to press the HMM database, and then load it with PyHMMER. However, most of the PyHMMER interface should accept unpressed HMMs as well, the gain is not that important as compared to HMMER the optimized profile can be built in parallel in different threads!
from pyhmmer.
Related Issues (20)
- `hmmscan` gets confused about short monotone sequences' alphabet. ( assumes `Amino`, actually `RNA`) HOT 7
- Scoring a set of sequences with HMM HOT 3
- Save the DigitalSequenceBlock as pickle HOT 6
- [Feature Request] Internally assigning Z for ```HMM``` class HOT 3
- cannot reproduce example for ```pyhmmer.hmmer.hmmsearch``` HOT 1
- Hmmsearch callback tqdm update HOT 4
- HMMSearch block and freeze HOT 5
- `pyhmmer.nhmmer` throws error when the number of FASTA seqs is larger than 64 HOT 2
- pyhmmer.hmmer.hmmsearch is always slower than using hmmsearch directly HOT 6
- Guess bit_cutoffs in hmmsearch
- Apply cutoffs for domains HOT 2
- [Question] What does does `included` and `reported` mean in pyhmmer.plan7.Hit? HOT 2
- [Bug] Pickling and unpickling an HMM object changes the cutoff values HOT 5
- [question] PyInfernal? HOT 3
- BUG: `plan7.HMM.validate()` fails to raise exceptions with ill formatted hmm profiles HOT 1
- Uninformative error when input hmm file contains profiles with different alphabets HOT 2
- PyHmmer sets CPU float behaviour globally, potentially causing issues in other libraries HOT 1
- "Erroneous" type warning? HOT 2
- Return a single TopHits object when passing a single hmm to hmmsearch
- Parameter to remove insert column in `hmmalign`
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pyhmmer.