Metadata-Version: 2.1
Name: dipwmsearch
Version: 0.1.0
Summary: A package dedicated to diPWM motif search into a text
Home-page: https://gite.lirmm.fr/rivals/dipwmsearch
Author: Marie Mille (main contributor), Bastien Cazaux, Julie Ripoll and Eric Rivals
Author-email: dipwm@lirmm.fr
License: UNKNOWN
Project-URL: Bug Tracker, https://gite.lirmm.fr/rivals/dipwmsearch/-/issues
Project-URL: Documentation, https://rivals.lirmm.net/dipwmsearch/
Project-URL: Team, http://www.lirmm.fr/recherche/equipes/mab
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: CeCILL-B Free Software License Agreement (CECILL-B)
Classifier: License :: OSI Approved :: CEA CNRS Inria Logiciel Libre License, version 2.1 (CeCILL-2.1)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: pytest
Requires-Dist: pyahocorasick

# Package `dipwmsearch`

## Description
Dedicated package to `dipwmsearch` through a text. Provides different approaches to seek for motifs (diPWM) through a text (for example a sequence) :
- sliding window (`search_semi_naive`)
- enumeration of valids words and AhoCorasick search of that set of words through the text (`search_aho`)
- enumeration of valids substrings, AhoCorasick search of that set of substrings through the text, and check each window (`search_block`)
- super alphabet search (`search_super`)

## Install
### Local installation using git

- clone the git repository
```bash
git clone git@gite.lirmm.fr:rivals/dipwmsearch.git
```
- go to the root of the folder
```bash
cd dipwmsearch
```

- use the `Makefile` to install
```bash
make install
```

### Installation using pip

```bash
pip install dipwmsearch
```


## Getting started

- To import the package
```python
import dipwmsearch as ds
```

- To parse a diPWM file and create an object diPWM
```python
diP = ds.create_diPwm(diPwm_path_file)
```

- To use the enumeration and Aho-Corasick search
```python
for start_position, word, score in ds.search_aho_ratio(diP, text, ratio):
	   print(f'{start_position}\t{word}\t{score}')
```

## Documentation
More info in the [documentation](https://rivals.lirmm.net/dipwmsearch/)

## License
License type: CeCILL-B
[More info](https://cecill.info/licences/Licence_CeCILL-B_V1-en.html)

## Authors

- Marie Mille (main contributor)
- Bastien Cazaux
- Julie Ripoll
- Eric Rivals

## Dependencies
### Basics to install
- `pyahocorasick`

### For tests
- `pytest`
- `pandas`


