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

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]])