Metadata-Version: 2.1
Name: dipwmsearch
Version: 0.1.1
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
Description: # 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`
        
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
