Metadata-Version: 2.4
Name: alvoc
Version: 0.1.0
Author-email: mshunjan <manjothunjan@gmail.com>
License-File: LICENSE
Requires-Python: <3.13,>=3.11
Requires-Dist: biopython<2.0,>=1.84
Requires-Dist: matplotlib<4.0.0,>=3.9.0
Requires-Dist: numpy<3.0.0,>=2.0.0
Requires-Dist: ortools<10.0.0,>=9.10.4067
Requires-Dist: pysam<1.0.0,>=0.22.1
Requires-Dist: scikit-learn<2.0.0,>=1.5.1
Requires-Dist: seaborn<1.0.0,>=0.13.2
Requires-Dist: typer<1.0.0,>=0.12.3
Description-Content-Type: text/markdown


<div style="display: flex; justify-content: center; align-items: center; text-align: center; flex-direction: column;">
  <div style="display: flex; align-items: center;">
    <img src="https://raw.githubusercontent.com/alvoc/alvoc/main/docs/assets/icon.svg" alt="Logo" width="200" height="auto">
    <span style="font-size: 100px; color: #4e8ada;"> Alvoc </span>
  </div>

  <p><em>Abundance learning for variants of concern</em></p>

  <div style="text-align: center;">
    <p>
      <a href="https://github.com/alvoc/alvoc/issues" target="_blank">Report Bug</a>
      |
      <a href="https://github.com/alvoc/alvoc/issues" target="_blank">Request Feature</a>
    </p>
    <p>
      <a href="https://alvoc.github.io" target="_blank"> Documentation </a>
    </p>
  </div> 
</div>

---

## Overview

Alvoc is used for estimating the abundace of variants of concern from wastewater sequencing data.

It can be used for:

* Converting nucleotide and amino acid mutations for a particular virus
* Determining the frequency of mutations of interest in BAM files
* Plotting the depth for each ARTIC amplicon
* Comparing amplicon GC content with its read depth (as a measure of degredation)

## Installation


### With Pip

Pip is the default package installer for Python.

1. Install [Python](https://www.python.org/downloads/). We recommend using [pyenv](https://github.com/pyenv/pyenv) for python version management.

2. Install it directly from source (main branch).

<!-- termynal -->
```console
$ pip install git+https://github.com/alvoc/alvoc.git@main
---> 100%
Done!
```

## Usage/Examples
 
[TBD]

# License
This project is licensed under the terms of the MIT license.