fileHandler.py

# fileHandler.py
# ----------
# HMM_TMRCA Project
# Licensing Information: Please do not distribute.
# You are free to use and extend these code for educational purposes.
# ProblemSet written by professor Yun S. Song
# Solution and code written by Jae Young Ryoo (jay.ryoo@gmail.com) and Saba Khalilnaji

import sys, math

"""
outputEstimatedParameters
INPUT: HMM model, fileName
OUTPUT: writes estimatedParameters in the correct form to fileName
"""
def outputEstimatedParameters(model, fileName):
    try:
        outputFile = open(fileName, 'w')
    except:
        print "File could not be opened"
    for i in model.getStates():
        outputFile.write('%d %.2e\n' % (i, model.p(i)))
    for i in model.getStates():
        for j in model.getStates():
            outputFile.write('%.2e' % model.a(i,j))
            if j != model.getStates()[len(model.getStates())-1]:
                outputFile.write(' ')
            else:
                outputFile.write('\n')
    for i in model.getStates():
        outputFile.write('%d %.2e %.2e\n' % (i, model.e(i,model.getEmissions()[0]), model.e(i,model.getEmissions()[1])))
    outputFile.close()

"""
outputLikelihoods
INPUT: (list) of likelihoods, fileName
OUTPUT: the likelihoods to fileName

"""
def outputLikelihoods(likelihoods, fileName):
    try:
        outputFile = open(fileName, 'w')
    except:
        print "File could not be opened"
    for i in likelihoods:
        outputFile.write('%.2e\n' % i)
    outputFile.close()


"""
outputDecodings
INPUT: (list) of tuple of decodings, fileName
OUTPUT: writes to fileName according to format laid out in README
"""
def outputDecodings(decodings, fileName):
    f = open(fileName, 'w')
    for v in decodings:
        f.write("%d %d %.2e\n" % v)
    f.close()