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Sourcecode: python-biopython version File versions


00001 """Generic functions which are useful for working with HMMs.

This just collects general functions which you might like to use in
dealing with HMMs.
# standard modules
import string

00009 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.

    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 = string.ljust(emission_title, title_length)
    real_title = string.ljust(real_title, title_length)
    predicted_title = string.ljust(predicted_title, title_length)

    cur_position = 0
    # while we still have more than seq_length characters to print
    while 1:
        if (cur_position + seq_length) < len(emissions):
            extension = seq_length
            extension = len(emissions) - cur_position
        print "%s%s" % (emission_title,
                        emissions.data[cur_position:cur_position + seq_length])
        print "%s%s" % (real_title,
                                        cur_position + seq_length])
        print "%s%s\n" % (predicted_title,
                                               cur_position + seq_length])

        if (len(emissions) < (cur_position + seq_length)):

        cur_position += seq_length


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