def wt_similarity(x, matrix='blosum62'):
x1 = x.peptide
x2 = x.wt
#print(x1,x2)
matrix = tepitope.get_matrix(matrix)
return tepitope.similarity_score(matrix, x1, x2)
def virus_similarity(x, matrix='blosum62'):
if x.virus_match is None:
return
x1 = x.peptide
x2 = x.virus_match
matrix = tepitope.get_matrix(matrix)
return tepitope.similarity_score(matrix, x1, x2)
Copyright (C) Damien Farrell
"""
from __future__ import absolute_import, print_function
import sys, os, subprocess
import time
import pickle
import numpy as np
import pandas as pd
pd.set_option('display.width', 150)
pd.set_option('max_colwidth', 80)
from collections import OrderedDict
from epitopepredict import base, config, analysis, sequtils, peptutils, tepitope
defaultpath = os.getcwd()
sim_matrix = tepitope.get_matrix('pmbec')
metrics = [
'score', 'matched_score', 'binding_diff', 'perc_rank', 'wt_similarity',
'self_similarity', 'virus_similarity', 'anchor', 'hydro', 'net_charge'
]
class NeoEpitopeWorkFlow(object):
"""Class for implementing a neo epitope workflow."""
def __init__(self, opts={}):
for i in opts:
self.__dict__[i] = opts[i]
return
def setup(self):
"""Setup main parameters"""