Metadata-Version: 2.1
Name: pwseqdist
Version: 0.1.1
Summary: Efficiently computes distances between protein sequences
Home-page: https://github.com/agartland/pwseqdist
Author: Andrew Fiore-Gartland
Author-email: agartlan@fredhutch.org
Maintainer: Andrew Fiore-Gartland
Maintainer-email: agartlan@fredhutch.org
License: MIT
Description: # pwseqdist
        
        [![Build Status](https://travis-ci.com/kmayerb/pwseqdist.svg?branch=master)](https://travis-ci.com/kmayerb/pwseqdist)
        
        A small package that efficiently computes distances between protein sequences.
        Can accommodate similarity matrices, sequences of different lengths and custom
        metrics.
        
        ## Install
        
        ```
        pip install pwseqdist
        ```
        
        ## Example
        
        ```python
        import pwseqdist as pw
        import multiprocessing
        from scipy.spatial.distance import squareform
        
        peptides = ['CACADLGAYPDKLIF','CACDALLAYTDKLIF',
                    'CACDAVGDTLDKLIF','CACDDVTEVEGDKLIF',
                    'CACDFISPSNWGIQSGRNTDKLIF','CACDPVLGDTRLTDKLIF']
        
        dvec = pw.apply_pairwise_sq(seqs = peptides, 
        			    metric = pw.metrics.nw_hamming_metric, 
        			    ncpus  = multiprocessing.cpu_count() )
        
        dmat = squareform(dvec).astype(int)
        dmat
        ```
        
        ```
        array([[ 0,  4,  6,  7, 15,  8],
               [ 4,  0,  5,  7, 14,  7],
               [ 6,  5,  0,  6, 14,  4],
               [ 7,  7,  6,  0, 14,  8],
               [15, 14, 14, 14,  0, 11],
               [ 8,  7,  4,  8, 11,  0]])
        ```
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
