crf-beam
Beam search for Bonito CRF models.
Usage
>>> import torch
>>> from crf_beam import beam_search
>>>
>>> T, C, S = 1000, 320, 64
>>> scores = torch.rand(T, C)
>>> back_guides = torch.rand(T + 1, S)
>>> post = torch.rand(T, S)
>>>
>>> sequence, qstring, moves = beam_search(scores, back_guides, post)
>>> sequence
'ACACTCGCAGCGCGATACGACTGATCGAGATATACTCAGTGTACACAGT...'
>>> qstring
'(&''(****95444"@732"55",--/5555"5"@@E"E4""","-#**...'
Developer Quickstart
Python
$ python3 -m venv venv3
$ source venv3/bin/activate
(venv3) $ pip install -r requirements.txt
(venv3) $ make build
(venv3) $ make test
WASM
$ make wasm
$ node tests/test.js
1 maintainer
Metadata
1 maintainer
Release files for crf-beam 0.1.9
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| crf_beam-0.1.9-cp311-cp311-manylinux2014_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.17+ x86-64 | Details |
| crf_beam-0.1.9-cp310-cp310-manylinux2014_x86_64.whl | CPython 3.10 | CPython 3.10 | Linux glibc 2.17+ x86-64 | Details |
| crf_beam-0.1.9-cp39-cp39-manylinux2014_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.17+ x86-64 | Details |
| crf_beam-0.1.9-cp38-cp38-manylinux2014_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.17+ x86-64 | Details |
Total release size: 11.6 MB
Release files / crf_beam-0.1.9-cp311-cp311-manylinux2014_x86_64.whl
| Download URL | crf_beam-0.1.9-cp311-cp311-manylinux2014_x86_64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.6
|
Release files / crf_beam-0.1.9-cp310-cp310-manylinux2014_x86_64.whl
| Download URL | crf_beam-0.1.9-cp310-cp310-manylinux2014_x86_64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.6
|
Release files / crf_beam-0.1.9-cp39-cp39-manylinux2014_x86_64.whl
| Download URL | crf_beam-0.1.9-cp39-cp39-manylinux2014_x86_64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.6
|
Release files / crf_beam-0.1.9-cp38-cp38-manylinux2014_x86_64.whl
| Download URL | crf_beam-0.1.9-cp38-cp38-manylinux2014_x86_64.whl |
|---|---|
| Size | 2.9 MB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/5.1.1 CPython/3.9.6
|
