scoreMatrix.py

import amino

aminoListChr = amino.getOrderedArray()

class ScoreMatrix:
	def __init__(self):
		self.mat = []
		for i in xrange(22):
			r = []
			for i in xrange(22):
				r.append('u') #initialize with 'u' for uninitialized
			self.mat.append(r)
		self.indexLookup = {}
		for i in xrange(len(aminoListChr)):
			self.indexLookup[aminoListChr[i]] = i
	def printMatrix(self):
		for i in self.mat:
			print i
	def get(self, v1, v2):
		#make sure v1p is always lower or equal to v2p
		v1p = v1 if ord(v1)<ord(v2) else v2
		v2p = v1 if ord(v1)>=ord(v2) else v2
		try:
			x = self.indexLookup[v1p]
			y = self.indexLookup[v2p]
		except KeyError:
			raise Exception('RuntimeException','Amino acid not defined '+ v1 + ' or ' + v2)
		if(self.mat[x][y] == 'u'):
			raise Exception('RuntimeException','Uninitialized amino acid pair')
		if(self.mat[x][y] == 'i'):
			raise Exception('RuntimeException','Amino acid invalidated')
		else:
			return self.mat[x][y]
	def set(self,v1,v2, score):
		v1p = v1 if ord(v1)<ord(v2) else v2
		v2p = v1 if ord(v1)>=ord(v2) else v2
		try:
			x = self.indexLookup[v1p]
			y = self.indexLookup[v2p]
		except KeyError:
			raise Exception('RuntimeException','Amino acid not defined')
		if(self.mat[x][y] == 'i'):
			raise Exception('RuntimeException','Amino acid invalidated')
		self.mat[x][y] = score

	def setInvalid(self,v):
		try:
			x = self.indexLookup[v]
		except KeyError:
			raise Excpetion('RuntimeException', 'Amino acid not defined')
		for i in xrange(len(aminoListChr)):
			self.mat[i][x] = 'i'
		for i in xrange(len(aminoListChr)):
			self.mat[x][i] = 'i'
			
	def fwrite(self, fname):
		f = open(fname,'w')
		for i in self.mat:
			line = ""
			for j in i:
				line += str(j) + ","
			f.write(line[0:-1] + '\n')
	def fread(self, fname):
		f = open(fname,'r')
		self.mat = []
		for i in f:
			self.mat.append(i.strip().split(','))