eff-len 0.1.0__tar.gz

eff_len-0.1.0/.github/workflows/publish.yml

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+name: Publish
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install build
+      - run: python -m build
+      - uses: pypa/gh-action-pypi-publish@release/v1

eff_len-0.1.0/.gitignore

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+__pycache__/
+*.egg-info/
+dist/
+build/
+.ipynb_checkpoints/

eff_len-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: eff-len
+Version: 0.1.0
+Summary: Spectral measure of diversity for multiple sequence alignments
+Project-URL: Homepage, https://github.com/vaiteaopuu/effective_length
+Project-URL: Issues, https://github.com/vaiteaopuu/effective_length/issues
+Author-email: Vaitea Opuu <vaitea.opuu@cnrs.fr>
+License-Expression: MIT
+Keywords: bioinformatics,diversity,msa,sequence-alignment
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Requires-Dist: numpy
+Description-Content-Type: text/markdown
+
+# eff_len
+
+Spectral measure of diversity for multiple sequence alignments.
+
+## Overview
+
+This repo contains the code to reproduce the results in *"A spectral framework for measuring diversity in multiple sequence alignments"*. It introduces a measure, `L_eff`, that estimates the diversity (or amount of information) contained in a multiple sequence alignment. `L_eff` allows a faithful comparison between MSAs, as well as between generated datasets.
+
+## Install
+
+Requirements: NumPy.
+
+```bash
+pip install eff_len
+```
+
+From source:
+
+```bash
+git clone https://github.com/vaiteaopuu/effective_length
+cd effective_length
+pip install .
+```
+
+## Usage
+
+### Python
+
+```python
+from eff_len import read_fasta, msa_to_oh, effective_length
+
+msa = read_fasta("data/RF00028.fa", seq_type="nuc")
+
+msa_oh = msa_to_oh(msa, seq_type="nuc")
+N, L, k = msa_oh.shape
+L_eff = effective_length(msa_oh)
+
+print(N, L, L_eff, L_eff / L)
+# 2611 251 35.88477058938092 0.14296721350350963
+```
+
+`cross_effective_length` and `leff` are also exported, for comparing two alignments and for the convenience wrapper respectively.
+
+## Repository content
+
+| Path | Description |
+| --- | --- |
+| `src/eff_len/` | The package itself |
+| `analysis/` | Notebooks and scripts |
+| `data/` | Example alignments |
+| `reproducibility.org` | Code snippets reproducing the figures in the paper |
+
+## Data sources
+
+The data used in these analyses were extracted from:
+
+- C. Lambert *et al.* (2025) *Nat. Commun.*
+- F. Calvanese *et al.* (2024) *NAR*
+- M. Mirdita *et al.* (2027) *NAR*
+
+## Citation
+
+If you use this code, please cite:
+
+```bibtex
+@article{opuu_spectral,
+  title   = {A spectral framework for measuring diversity in multiple sequence alignments},
+  author  = {Opuu, Vaitea},
+  year    = {2026}
+}
+```
+
+## License
+
+MIT

eff_len-0.1.0/README.md

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+# eff_len
+
+Spectral measure of diversity for multiple sequence alignments.
+
+## Overview
+
+This repo contains the code to reproduce the results in *"A spectral framework for measuring diversity in multiple sequence alignments"*. It introduces a measure, `L_eff`, that estimates the diversity (or amount of information) contained in a multiple sequence alignment. `L_eff` allows a faithful comparison between MSAs, as well as between generated datasets.
+
+## Install
+
+Requirements: NumPy.
+
+```bash
+pip install eff_len
+```
+
+From source:
+
+```bash
+git clone https://github.com/vaiteaopuu/effective_length
+cd effective_length
+pip install .
+```
+
+## Usage
+
+### Python
+
+```python
+from eff_len import read_fasta, msa_to_oh, effective_length
+
+msa = read_fasta("data/RF00028.fa", seq_type="nuc")
+
+msa_oh = msa_to_oh(msa, seq_type="nuc")
+N, L, k = msa_oh.shape
+L_eff = effective_length(msa_oh)
+
+print(N, L, L_eff, L_eff / L)
+# 2611 251 35.88477058938092 0.14296721350350963
+```
+
+`cross_effective_length` and `leff` are also exported, for comparing two alignments and for the convenience wrapper respectively.
+
+## Repository content
+
+| Path | Description |
+| --- | --- |
+| `src/eff_len/` | The package itself |
+| `analysis/` | Notebooks and scripts |
+| `data/` | Example alignments |
+| `reproducibility.org` | Code snippets reproducing the figures in the paper |
+
+## Data sources
+
+The data used in these analyses were extracted from:
+
+- C. Lambert *et al.* (2025) *Nat. Commun.*
+- F. Calvanese *et al.* (2024) *NAR*
+- M. Mirdita *et al.* (2027) *NAR*
+
+## Citation
+
+If you use this code, please cite:
+
+```bibtex
+@article{opuu_spectral,
+  title   = {A spectral framework for measuring diversity in multiple sequence alignments},
+  author  = {Opuu, Vaitea},
+  year    = {2026}
+}
+```
+
+## License
+
+MIT

eff_len-0.1.0/data/Azo/azo_exp.str

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