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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Generic functions which are useful for working with HMMs.
This just collects general functions which you might like to use in
dealing with HMMs.
"""
from __future__ import print_function
def pretty_print_prediction(emissions, real_state, predicted_state,
emission_title="Emissions",
real_title="Real State",
predicted_title="Predicted State",
line_width=75):
"""Print out a state sequence prediction in a nice manner.
Arguments:
o emissions -- The sequence of emissions of the sequence you are
dealing with.
o real_state -- The actual state path that generated the emissions.
o predicted_state -- A state path predicted by some kind of HMM model.
"""
# calculate the length of the titles and sequences
title_length = max(len(emission_title), len(real_title),
len(predicted_title)) + 1
seq_length = line_width - title_length
# set up the titles so they'll print right
emission_title = emission_title.ljust(title_length)
real_title = real_title.ljust(title_length)
predicted_title = predicted_title.ljust(title_length)
cur_position = 0
# while we still have more than seq_length characters to print
while True:
if (cur_position + seq_length) < len(emissions):
extension = seq_length
else:
extension = len(emissions) - cur_position
print("%s%s" % (emission_title,
emissions[cur_position:cur_position + seq_length]))
print("%s%s" % (real_title,
real_state[cur_position:cur_position + seq_length]))
print("%s%s\n" % (predicted_title,
predicted_state[cur_position:
cur_position + seq_length]))
if (len(emissions) < (cur_position + seq_length)):
break
cur_position += seq_length
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