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# Copyright 2001 Brad Chapman. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause 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.
"""
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:
- emissions -- The sequence of emissions of the sequence you are
dealing with.
- real_state -- The actual state path that generated the emissions.
- 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(f"{emission_title}{emissions[cur_position:cur_position + seq_length]}")
print(f"{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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