Metadata-Version: 2.1
Name: konstel
Version: 0.8.1
Summary: Hash-based phonemic sequence identifiers
Home-page: http://github.com/bede/konstel
Author: Bede Constantinides
Author-email: bedeabc@gmail.com
License: LICENSE
Description: # Konstel(lations)
        
        [![Tests](https://img.shields.io/github/workflow/status/bede/konstel/tests)](https://github.com/bede/konstel/actions)
        [![PyPI](https://img.shields.io/pypi/v/konstel.svg?color=brightgreen)](https://badge.fury.io/py/konstel)
        
        **Not yet stable, proceed with caution**
        
        An extensible command line tool and library for generating memorable and pronounceable hash-based identifier schemes for sequences, biological or otherwise. For further details and my SARS-CoV-2 naming proposal, please read my [blog post](https://log.bede.im/2021/01/19/covid-hashes). Requires Python 3.6+.
        
        ### SARS-CoV-2 naming
        
        Phonemic and truncated cbase32 identifiers provide 36 and 40 bits of entropy respectively, producing no collisions within publicly deposited SARS-CoV-2 spike protein sequences as of 2021-04-12.
        
        ## Install
        
        Ideally inside a new virtualenv or conda environment:
        
        ```shell
        # Latest release
        pip install konstel
        
        # Development version
        git clone https://github.com/bede/konstel
        pip install --editable konstel
        ```
        
        
        ## Usage 
        
        ### Command line
        
        ```bash
        $ konstel gen sars-cov-2-s.genome konstel/tests/data/spike.genome.fa --output table
        scheme               sars-cov-2-s   
        hash                 S:0k8n9hjh5xh5kbef1k6ye7e2d4brhpry5r985avrtf69v6amrbc0
        hash-8               S:0k8n9hjh     
        id                   S:huhiji-gakihi  
        
        $ echo "ACGT" | konstel gen generic.nucl - --output table
        scheme               generic        
        hash                 3qzkx17yf1vy0ssvd6xxvkt02973jvhzk51xv28cj6va16pvkbr0
        id                   bituzu-gupahu-zolodu-lumaki-suripi-rozitu-guhabi-figogo
        ```
        
        
        ### Python
        
        ```python
        >>> from konstel import konstel
        >>> konstel.generate('sars-cov-2-s.protein', 'konstel/tests/data/spike.prot.fa')
        {'scheme': 'sars-cov-2-s', 'hash': 'S:0k8n9hjh5xh5kbef1k6ye7e2d4brhpry5r985avrtf69v6amrbc0', 'hash-8': 'S:0k8n9hjh', 'id': 'S:huhiji-gakihi'}
        ```
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Requires-Python: >=3.6
Description-Content-Type: text/markdown
