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#29 Moved tables for BLOSUM62 and PAM250
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@weka511
weka511 committed Mar 13, 2023
1 parent 343f23b commit 7c56276
Showing 1 changed file with 97 additions and 21 deletions.
118 changes: 97 additions & 21 deletions reference_tables.py
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#!/usr/bin/env python
# Copyright (C) 2015-2020 Greenweaves Software Limited

# Copyright (C) 2015-2023 Greenweaves Software Limited

# This is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
Expand All @@ -14,10 +15,16 @@
# You should have received a copy of the GNU General Public License
# along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>

# This file contains a collection of functions to solve the problems
# at rosalind.info.
'''
This file contains a reference data, such as scoring masses and codon tables,
to solve the problems at rosalind.info.
'''

from abc import ABC
from re import compile
from unittest import TestCase, main
import numpy as np

import re
bases='ACGT'

codon_table={
Expand Down Expand Up @@ -102,7 +109,7 @@ def asInteger(self):
# Lookup table for amino acids, from
# https://en.wikipedia.org/wiki/Proteinogenic_amino_acid#Mass_spectrometry

amino_acids={
amino_acids = {
'A': AminoAcid('Alanine', 'A', 'Ala', 71.03711, 71.0788),
'C': AminoAcid('Cysteine', 'C', 'Cys', 103.00919, 103.1388),
'D': AminoAcid('Aspartic acid', 'D', 'Asp', 115.02694, 115.0886),
Expand Down Expand Up @@ -134,35 +141,104 @@ def asInteger(self):
'T': 0
}

def createSimpleDNASubst(match=+1,subst=1,bases='ATGC'):
'''
createSimpleDNASubst
Populate a simple scoring table

# createSimpleDNASubst
#
# Populate a simple scoring table

# Inputs: match Reward for matching
# subst Penalty for a mismatch
# bases Replace with 'AUGC' for RNA
def createSimpleDNASubst(match=+1,subst=1,bases='ATGC'):
Inputs:
match Reward for matching
subst Penalty for a mismatch
bases Replace with 'AUGC' for RNA
'''
weights={}
for i in range(len(bases)):
for j in range(len(bases)):
weights[(bases[i],bases[j])] = +match if i==j else -subst
return weights

# get_re_protein
# Produce a regular expression to recognize a straing of amino acids

def get_re_protein(min_length=1):
return re.compile('[A,C-IK-WY]{'+str(min_length)+',}')
'''
get_re_protein
Produce a regular expression to recognize a straing of amino acids
'''
return compile('[A,C-IK-WY]{'+str(min_length)+',}')


class ScoringMatrix(ABC):
'''
Abstract class representing scoring matrices
'''
def __init__(self,score,
index=['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']):
self.index = index
self.score = score
def get_score(self,a,b):
'''
Determins score when a is matched with b
'''
return self.score[self.index.index(a), self.index.index(b)]

class BLOSUM62(ScoringMatrix):
'''
BLOSUM 62 scoring matrix as presented in Rosalind
'''
def __init__(self):
super().__init__(
np.array([[4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2],
[ 0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2],
[-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3],
[-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2],
[-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3],
[ 0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3],
[-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2],
[-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1],
[-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2],
[-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1],
[-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1],
[-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2],
[-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3],
[-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1],
[-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2],
[ 1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2],
[ 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2],
[ 0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1],
[-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2],
[-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7]]))

class PAM250(ScoringMatrix):
'''
BLOSUM 62 scoring matrix as presented in Rosalind
'''
def __init__(self):
super().__init__(
np.array([[2, -2, 0, 0, -3, 1, -1, -1, -1, -2, -1, 0, 1, 0, -2, 1, 1, 0, -6, -3],
[-2, 12, -5, -5, -4, -3, -3, -2, -5, -6, -5, -4, -3, -5, -4, 0, -2, -2, -8, 0],
[0, -5, 4, 3, -6, 1, 1, -2, 0, -4, -3, 2, -1, 2, -1, 0, 0, -2, -7, -4],
[0, -5, 3, 4, -5, 0, 1, -2, 0, -3, -2, 1, -1, 2, -1, 0, 0, -2, -7, -4],
[-3, -4, -6, -5, 9, -5, -2, 1, -5, 2, 0, -3, -5, -5, -4, -3, -3, -1, 0, 7],
[1, -3, 1, 0, -5, 5, -2, -3, -2, -4, -3, 0, 0, -1, -3, 1, 0, -1, -7, -5],
[-1, -3, 1, 1, -2, -2, 6, -2, 0, -2, -2, 2, 0, 3, 2, -1, -1, -2, -3, 0],
[-1, -2, -2, -2, 1, -3, -2, 5, -2, 2, 2, -2, -2, -2, -2, -1, 0, 4, -5, -1],
[-1, -5, 0, 0, -5, -2, 0, -2, 5, -3, 0, 1, -1, 1, 3, 0, 0, -2, -3, -4],
[-2, -6, -4, -3, 2, -4, -2, 2, -3, 6, 4, -3, -3, -2, -3, -3, -2, 2, -2, -1],
[-1, -5, -3, -2, 0, -3, -2, 2, 0, 4, 6, -2, -2, -1, 0, -2, -1, 2, -4, -2],
[0, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 2, 0, 1, 0, 1, 0, -2, -4, -2],
[1, -3, -1, -1, -5, 0, 0, -2, -1, -3, -2, 0, 6, 0, 0, 1, 0, -1, -6, -5],
[0, -5, 2, 2, -5, -1, 3, -2, 1, -2, -1, 1, 0, 4, 1, -1, -1, -2, -5, -4],
[-2, -4, -1, -1, -4, -3, 2, -2, 3, -3, 0, 0, 0, 1, 6, 0, -1, -2, 2, -4],
[1, 0, 0, 0, -3, 1, -1, -1, 0, -3, -2, 1, 1, -1, 0, 2, 1, -1, -2, -3],
[1, -2, 0, 0, -3, 0, -1, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, 0, -5, -3],
[0, -2, -2, -2, -1, -1, -2, 4, -2, 2, 2, -2, -1, -2, -2, -1, 0, 4, -6, -2],
[-6, -8, -7, -7, 0, -7, -3, -5, -3, -2, -4, -4, -6, -5, 2, -2, -5, -6, 17, 0],
[-3, 0, -4, -4, 7, -5, 0, -1, -4, -1, -2, -2, -5, -4, -4, -3, -3, -2, 0, 10]]))

if __name__=='__main__':
import unittest

class Test_Amino_acids(unittest.TestCase):
class Test_Amino_acids(TestCase):
def test_match_integer(self):
for key in integer_masses:
self.assertEqual(integer_masses[key],amino_acids[key].asInteger())

unittest.main()
main()

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