Created
February 20, 2012 16:42
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#!/usr/bin/env python | |
# Usage: python blosum.py blosum62.txt | |
# Then, enter input in "row col" format -- e..g, "s f". | |
import sys | |
class InvalidPairException(Exception): | |
pass | |
class Matrix: | |
def __init__(self, matrix_filename): | |
self._load_matrix(matrix_filename) | |
def _load_matrix(self, matrix_filename): | |
with open(matrix_filename) as matrix_file: | |
matrix = matrix_file.read() | |
lines = matrix.strip().split('\n') | |
header = lines.pop(0) | |
columns = header.split() | |
matrix = {} | |
for row in lines: | |
entries = row.split() | |
row_name = entries.pop(0) | |
matrix[row_name] = {} | |
if len(entries) != len(columns): | |
raise Exception('Improper entry number in row') | |
for column_name in columns: | |
matrix[row_name][column_name] = entries.pop(0) | |
self._matrix = matrix | |
def lookup_score(self, a, b): | |
a = a.upper() | |
b = b.upper() | |
if a not in self._matrix or b not in self._matrix[a]: | |
raise InvalidPairException('[%s, %s]' % (a, b)) | |
return self._matrix[a][b] | |
def run_repl(matrix): | |
while True: | |
try: | |
user_input = input('>>> ').strip() | |
except (EOFError, KeyboardInterrupt) as e: | |
print() | |
return | |
if user_input.lower() in ['q', 'exit', 'quit']: | |
return | |
components = user_input.split() | |
if len(components) != 2: | |
continue | |
try: | |
print(matrix.lookup_score(components[0], components[1])) | |
except InvalidPairException: | |
continue | |
def main(): | |
if len(sys.argv) != 2: | |
sys.exit('Usage: %s [matrix filename]') | |
matrix_filename = sys.argv[1] | |
matrix = Matrix(matrix_filename) | |
run_repl(matrix) | |
if __name__ == '__main__': | |
main() |
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A R N D C Q E G H I L K M F P S T W Y V B Z X * | |
A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 | |
R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 | |
N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 | |
D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 | |
C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 | |
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 | |
E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 | |
G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 | |
H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 | |
I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 | |
L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 | |
K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 | |
M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 | |
F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 | |
P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 | |
S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 | |
T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 | |
W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 | |
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 | |
V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 | |
B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 | |
Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 | |
X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 | |
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1 |
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