Metadata-Version: 2.4
Name: kontiguity
Version: 0.0.1
Summary: Eukaryotic contigs retrieval and classification tool.
Project-URL: Homepage, https://github.com/Mae-4815162342/kontiguity
Project-URL: Issues, https://github.com/Mae-4815162342/kontiguity/issues
Author-email: Maelys Delouis <maelys.delouis@pasteur.fr>
License: CC BY-NC 4.0
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
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Description-Content-Type: text/markdown

# Kontiguity: tool for eukaryotes contigs retrieval from genomic data and classification

Kontiguity is a python and bash pipeline created to retrieve unidentified contigs from eukaryotes genomic data, and to classify said contigs based on genomic contact data (Hi-C).

## Installation

```bash
pip install kontiguity
```

For development:

```bash
git clone https://github.com/Mae-4815162342/kontiguity.git
cd kontiguity
pip install -e .
```

## Presenting pipeline

Kontiguity is based on a pipeline of three subfunctions:

- **load** which serves data retrieval and formating, and provides a scrapping method to build a dataset from DToL (ref to add).

- **retrieve** for the retrieval of new contigs from WGS reads aligned on a reference genome (by default produces Hi-C maps for the further step, can be deactivated).

- **classify** for the contigs contacts classification, based on a plasmid-detection-oriented model at this day (a larger model can be provided later.)

Those three functions can be called individually or in order with the **pipeline** command, which provides an option to start at any step.

## Usage

### Loading a dataset

```bash
kontiguity load -n Saccaromyces_cerevisiae -r S_cerevisiae.fa 
```


## Outputs

TODO

## Classification model

TODO