Metadata-Version: 2.1
Name: AlleleFinder
Version: 0.3.6
Home-page: https://github.com/OLC-Bioinformatics/AlleleFinder
Author: Adam Koziol
Author-email: adam.koziol@inspection.gc.ca
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.9
Classifier: Development Status :: 5 - Production/Stable
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython ==1.81
Requires-Dist: click ==8.1.3
Requires-Dist: coloredlogs ==15.0.1
Requires-Dist: genemethods ==0.0.0.61
Requires-Dist: geneseekr ==0.5.0
Requires-Dist: genewrappers ==0.0.0.10
Requires-Dist: numpy ==1.26.4
Requires-Dist: OLCTools ==1.3.5
Requires-Dist: psutil ==5.9.4
Requires-Dist: pytest ==7.2.1
Requires-Dist: pytest-cov ==4.0.0
Requires-Dist: seaborn ==0.12.2
Requires-Dist: setuptools ==69.0.3
Requires-Dist: xlsxwriter ==3.0.2

# AlleleFinder

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## Overview

AlleleFinder is a Python-based suite of tools designed for the discovery, sequence typing, and profiling of _stx_ alleles in Shiga toxin-producing _Escherichia coli_ (STEC). It provides a comprehensive solution for researchers and professionals working in the field of bacterial genomics.

## Features

AlleleFinder offers seven main functionalities, each represented by a separate script:

1. [`profile_reduce`](https://olc-bioinformatics.github.io/AlleleFinder/profile_reduce): Reduces full wgMLST profile from Enterobase using genes of interest.
2. [`allele_translate_reduce`](https://olc-bioinformatics.github.io/AlleleFinder/allele_translate_reduce): Translates allele files from Enterobase in nucleotide format to amino acid, performs content and length checks, and removes duplicates.
3. [`allele_find`](https://olc-bioinformatics.github.io/AlleleFinder/allele_find): Performs BLAST analyses on a nucleotide allele database against nucleotide query sequences to discover their sequence types.
4. [`allele_translate_find`](https://olc-bioinformatics.github.io/AlleleFinder/allele_translate_find): Performs BLAST analyses on an amino acid database against amino acid query sequences to find matching alleles.
5. [`aa_allele_find`](https://olc-bioinformatics.github.io/AlleleFinder/aa_allele_find): Performs BLAST analyses on an amino acid database against amino acid query sequences to find matching alleles.
6. [`allele_split`](https://olc-bioinformatics.github.io/AlleleFinder/allele_split): Splits a single allele database file into multiple files; one sequence per file.
7. [`allele_concatenate`](https://olc-bioinformatics.github.io/AlleleFinder/allele_concatenate): Concatenates alleles of the _stx_ A and B subunits into a single sequence with a linker.

## Documentation

Detailed documentation for each script and general usage of AlleleFinder is available at the [AlleleFinder GitHub pages site](https://olc-bioinformatics.github.io/AlleleFinder/).

## Quick Start

[`Conda`](https://docs.conda.io/en/latest/) is required to install AlleleFinder. See the [documentation](http://bioconda.github.io/) or [AlleleFinder installation](https://olc-bioinformatics.github.io/AlleleFinder/install/) for instructions on getting conda installed on your system.

Create a new conda environment:

```bash
conda create -n allele_finder -c olcbioinformatics allelefinder
```

Additional installation instructions are available [here](https://olc-bioinformatics.github.io/AlleleFinder/installation).

## Usage

Each script has specific input requirements and usage instructions. Please refer to the respective documentation for each script for detailed information:

- [`profile_reduce`](https://olc-bioinformatics.github.io/AlleleFinder/profile_reduce)
- [`allele_translate_reduce`](https://olc-bioinformatics.github.io/AlleleFinder/allele_translate_reduce)
- [`allele_find`](https://olc-bioinformatics.github.io/AlleleFinder/allele_find)
- [`allele_translate_find`](https://olc-bioinformatics.github.io/AlleleFinder/allele_translate_find)
- [`aa_allele_find`](https://olc-bioinformatics.github.io/AlleleFinder/aa_allele_find)
- [`allele_split`](https://olc-bioinformatics.github.io/AlleleFinder/allele_split)
- [`allele_concatenate`](https://olc-bioinformatics.github.io/AlleleFinder/allele_concatenate)

## Feedback

We welcome your feedback. If you encounter any issues installing or running AlleleFinder, have feature requests, or need assistance, please [open an issue on GitHub](https://github.com/OLC-Bioinformatics/AlleleFinder/issues/new/choose).

## License

AlleleFinder is licensed under the MIT License. See the [LICENSE](https://github.com/OLC-Bioinformatics/AlleleFinder/blob/main/LICENSE) file for more details.
