entropy-analysis

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# Copyright (C) 2010 - 2012, A. Murat Eren
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Please read the COPYING file.

import sys 

try:
    import Oligotyping
except ImportError:
    import inspect
    print('''
    Oligotyping package seems to be missing from your PYTHONPATH. Running this may help:

        export PYTHONPATH="$PYTHONPATH:%s"

    ''' % (os.path.realpath(os.path.abspath(os.path.split(inspect.getfile(inspect.currentframe()))[0]))))
    sys.exit()

from Oligotyping.utils.utils import import_error

try:
    import matplotlib
except ImportError as e:
    import_error(e)
    sys.exit()

try:
    import matplotlib.pyplot as plt
except RuntimeError:
    print('''
    matplotlib is failing to connect to any X server for its GTK display. Please
    add the following directive into the 'matplotlibrc' file (which should be
    under '~/.matplotlib/' directory, if there is no such file, you should
    create one):

    backend: Agg

    ''')
    sys.exit()

try:
    from Oligotyping.utils import parsers
    from Oligotyping.lib.entropy import entropy_analysis
    from Oligotyping.lib.entropy import EntropyError
    from Oligotyping.utils.utils import process_command_line_args_for_quality_files
    from Oligotyping.visualization.entropy_distribution_bar import entropy_distribution_bar
except ImportError as e:
    import_error(e)
    sys.exit()

if __name__ == '__main__':
    if '--version' in sys.argv:
        print(parsers.version)
        sys.exit()

    parser = parsers.entropy()
    args = parser.parse_args()

    # process qual scores if provided
    qual_stats_dict = process_command_line_args_for_quality_files(args, _return = 'qual_stats_dict')       

    # the same file path is also used for the figure (e.g. output_file_path + '.png' or
    # output_file_path + '.pdf')
    output_file_path = args.alignment + '%s-ENTROPY' % ('-WEIGHTED' if args.weighted else '')

    try:
        entropy_values = entropy_analysis(args.alignment,
                                         output_file = output_file_path,
                                          uniqued = args.uniqued,
                                          weighted = args.weighted,
                                          qual_stats_dict = qual_stats_dict,
                                          amino_acid_sequences = args.amino_acid_sequences)
    except EntropyError as e:
        print("Something went wrong. Here is what we know:\n\n\t%s\n\n" % e)
        sys.exit(-1)

    entropy_distribution_bar(args.alignment,
                             entropy_values,
                             output_file = output_file_path,
                             quick = args.quick,
                             no_display = args.no_display,
                             qual_stats_dict = qual_stats_dict,
                             weighted = args.weighted,
                             verbose = True)