dipwmsearch 0.0.1

A package dedicated to diPWM motif search into a text

Package diPWM_search

Description

Dedicated package to diPWM_search 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)
• super alphabet search (search_super)

Install

Local installation using git

• clone the git repository

git clone [e-mail]:rivals/dipwmsearch.git

• go to the root of the folder

cd dipwm_search

• use the Makefile to install

make install

Installation using pip

....

Getting started

• To import the package

import dipwm_search as ds

• To parse a diPWM file and create an object diPWM

diP = ds.create_diPwm(diPwm_path_file)

• To use the enumeration and Aho-Corasick search

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

License

License type: CeCILL-B More info

Authors

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

Dependencies

Basics to install

• pyahocorasick

For tests

• pytest
• pandas