def loadMatrix(fn='blosum50.txt'):
FH = open(fn,'r')
data = FH.read()
FH.close()
L = data.strip().split('\n')
# matrix has metadata lines beginning w/'#'
# also has extra rows,cols for 'BZX*'
L = [e for e in L if not e[0] in '#BZX*']
# the last 4 cols are also 'BZX*'
L = [e.split()[:-4] for e in L]
aaNames = L.pop(0)
# each row also starts with the AA name
L = [t[1:] for t in L]
M = dict()
for i in range(len(aaNames)):
for j in range(len(aaNames)):
k = aaNames[i] + aaNames[j]
M[k] = int(L[i][j])
return aaNames,M
def showM(M,aaNames):
#each element takes up 4 spaces
print ' ' + ' '.join(aaNames)
for i,aa1 in enumerate(aaNames):
print aa1,
L = list()
for j in range(i+1):
aa2 = aaNames[j]
k = aa1 + aa2
L.append(str(M[k]).rjust(4))
print ''.join(L)
for aa1 in aaNames:
for aa2 in aaNames:
assert M[aa1+aa2] == M[aa2+aa1],aa1+aa2
if __name__ == '__main__':
aaNames,M = loadMatrix(fn='blosum50.txt')
showM(M,aaNames) |
