A package dedicated to diPWM motif search into a text
Project description
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 git@gite.lirmm.fr:rivals/dipwmsearch.git
- go to the root of the folder
cd dipwm_search
- use the
Makefile
to install
make install
Installation using pip
pip install dipwmsearch
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
dipwmsearch-0.0.3.tar.gz
(29.8 kB
view hashes)
Built Distribution
Close
Hashes for dipwmsearch-0.0.3-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c4f097e3248aadac9fef876da90a6898f837e8eb6c9dbf9b9e65d8cdd0feccbb |
|
MD5 | 1aaf1ae244acb7dd9e73eb5c1807c4c2 |
|
BLAKE2b-256 | 45dce3b2c2e1d83af07644681acae4f69bdd11f023e08045606cacae8083f203 |