A package dedicated to diPWM motif search into a text
Project 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
git clone git@gite.lirmm.fr:rivals/dipwmsearch.git
- go to the root of the folder
cd dipwmsearch
- use the
Makefile
to install
make install
Installation using pip
pip install dipwmsearch
Getting started
- To import the package
import dipwmsearch 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
Project details
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