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]])
2 maintainers
Metadata
2 maintainers
Release files for pwseqdist 0.6
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| pwseqdist-0.6-py3-none-any.whl | Python 3 | none | any | Details for pwseqdist-0.6-py3-none-any.whl |
Total release size: 53.6 kB
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