o-generate-html-output

#!/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 os
import sys
import pickle
import argparse

parser = argparse.ArgumentParser(description='Generate Static HTML Output from MED or Oligotyping runs')
parser.add_argument('run_info_dict_path', metavar = 'DICT', help = 'Serialized run info dictionary (RUNINFO.cPickle)')
parser.add_argument('type', metavar = '[oligotyping | med]', help = 'Type of analysis')
parser.add_argument('-o', '--output-directory', default = None, metavar = 'OUTPUT_DIR',\
                    help = 'Output directory for HTML output to be stored')
parser.add_argument('--entropy-figure', default = None, metavar = 'ENTROPY_FIGURE',\
                    help = 'Path for entropy figure *without* the file extension (e.g. only "/path/to/entropy" \
                           for "/path/to/entropy.png")')

args = parser.parse_args()

if args.type not in ['oligotyping', 'med']:
    print("Run type must be either 'oligotyping' or 'med'")
    sys.exit()

if not os.path.exists(args.run_info_dict_path):
    print("Runinfo file is not where you said it would be: '%s'" % args.run_info_dict_path)
    sys.exit()

run_info_dict = pickle.load(open(args.run_info_dict_path))

if args.type == 'oligotyping':
    from Oligotyping.utils.html.for_oligotyping import generate_html_output
    index_page = generate_html_output(run_info_dict, args.output_directory, args.entropy_figure) 
else:
    from Oligotyping.utils.html.for_decomposition import generate_html_output
    index_page = generate_html_output(run_info_dict, args.output_directory) 


print('\n\tHTML output is ready: "%s"\n' % index_page)