Sequence logo generator for aligned FASTA files
Project description
tlogo
Sequence logo generator for aligned FASTA files with HxB2 coordinate mapping for HIV Env.
Install
pip install tlogo
Development
git clone https://github.com/tmsincomb/tlogo.git
cd tlogo
pip install -e ".[dev]"
Usage
# Standard logo at specific HxB2 positions
tlogo logo alignment.fasta --positions 130,160,332
# Logo for an entire Env region
tlogo logo alignment.fasta --region V3
# Per-animal window logo around a single position
tlogo window alignment.fasta --position 100 --radius 7
# Auto-detect variant positions and generate window logos
tlogo auto alignment.fasta --variant-freq 0.5
Testing
pytest -v
Releasing
Version is managed automatically by setuptools-scm from git tags:
git tag v0.1.0
git push origin v0.1.0
PyPI publishing is handled by GitHub Actions via trusted publishing (OIDC). Configure your PyPI project to trust the publish.yml workflow.
License
MIT
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file tlogo-0.1.2.dev0.tar.gz.
File metadata
- Download URL: tlogo-0.1.2.dev0.tar.gz
- Upload date:
- Size: 304.7 kB
- Tags: Source
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
e481bbe66d2e749ec871ba3b910f1566bd58154015a0855e971ee531f4c70adb
|
|
| MD5 |
c8af376cbfb7bf5868b4cf957f3d66c5
|
|
| BLAKE2b-256 |
ef90440f218fbe93fd468caaa67e0d3f60b016cf9e3b972959da7edd0a8ed498
|
Provenance
The following attestation bundles were made for tlogo-0.1.2.dev0.tar.gz:
Publisher:
publish.yml on tmsincomb/tlogo
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
tlogo-0.1.2.dev0.tar.gz -
Subject digest:
e481bbe66d2e749ec871ba3b910f1566bd58154015a0855e971ee531f4c70adb - Sigstore transparency entry: 1002872374
- Sigstore integration time:
-
Permalink:
tmsincomb/tlogo@8a81ed2c257f3dab6b95d4b8384122d7f7419f3c -
Branch / Tag:
refs/tags/v0.1.1 - Owner: https://github.com/tmsincomb
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@8a81ed2c257f3dab6b95d4b8384122d7f7419f3c -
Trigger Event:
push
-
Statement type:
File details
Details for the file tlogo-0.1.2.dev0-py3-none-any.whl.
File metadata
- Download URL: tlogo-0.1.2.dev0-py3-none-any.whl
- Upload date:
- Size: 19.0 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? Yes
- Uploaded via: twine/6.1.0 CPython/3.13.7
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
72852cbd1e055a71f8a8da9dd8bacd3f4a7bb48d998ce8e85578b78d1b95e583
|
|
| MD5 |
eabae370eb98dc00e796aeb11c18abcd
|
|
| BLAKE2b-256 |
3b799bf01f096f803ce3d7823eb8a00aa214e6fcd8a6dce426cc8cc930b5a1f1
|
Provenance
The following attestation bundles were made for tlogo-0.1.2.dev0-py3-none-any.whl:
Publisher:
publish.yml on tmsincomb/tlogo
-
Statement:
-
Statement type:
https://in-toto.io/Statement/v1 -
Predicate type:
https://docs.pypi.org/attestations/publish/v1 -
Subject name:
tlogo-0.1.2.dev0-py3-none-any.whl -
Subject digest:
72852cbd1e055a71f8a8da9dd8bacd3f4a7bb48d998ce8e85578b78d1b95e583 - Sigstore transparency entry: 1002872377
- Sigstore integration time:
-
Permalink:
tmsincomb/tlogo@8a81ed2c257f3dab6b95d4b8384122d7f7419f3c -
Branch / Tag:
refs/tags/v0.1.1 - Owner: https://github.com/tmsincomb
-
Access:
public
-
Token Issuer:
https://token.actions.githubusercontent.com -
Runner Environment:
github-hosted -
Publication workflow:
publish.yml@8a81ed2c257f3dab6b95d4b8384122d7f7419f3c -
Trigger Event:
push
-
Statement type:
