make_prefs_file.py

#!/usr/bin/env python
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jesse Stombaugh","Jeremy Widmann", "Antonio Gonzalez Pena"]
__license__ = "GPL"
__version__ = "1.7.0"
__maintainer__ = "Jesse Stombaugh"
__email__ = "jesse.stombaugh@colorado.edu"
__status__ = "Release"

from qiime.util import make_option
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.format import build_prefs_string
from qiime.colors import get_map
from qiime.parse import parse_taxa_summary_table

options_lookup = get_options_lookup()

script_info={}
script_info['brief_description']="""Generate preferences file"""
script_info['script_description']="""This script generates a preferences (prefs) file, which can be passed to make_distance_histograms.py, make_2d_plots.py and make_3d_plots.py. The prefs file allows for defining the monte_carlo distance, gradient coloring of continuous values in the 2D and 3D plots, the ball size scale for all the samples and the color of the arrow and the line of the arrow for the procrustes analysis. Currently there is only one color gradient: red to blue."""
script_info['script_usage']=[]
script_info['script_usage'].append(("""Examples:""","""To make a prefs file, the user is required to pass in a user-generated mapping file using "-m" and an output filepath, using "-o". When using the defaults, the script will use ALL categories from the mapping file, set the background to black and the monte_carlo distances to 10.""","""%prog -m mapping.txt -o prefs_out.txt"""))
script_info['script_usage'].append(("""""","""If the user would like to use specified categories ('SampleID,Individual') or combinations of categories ('SampleID&&Individual'), they will need to use the -b option, where each category is comma delimited, as follows:""","""%prog -m mapping.txt -b "SampleID,Treatment,SampleID&&Treatment" -o prefs_out_1.txt"""))
script_info['script_usage'].append(("""""","""If the user would like to change the background color for their plots, they can pass the '-k' option, where the colors: black and white can be used for 3D plots and many additional colors can be used for the 2D plots, such as cyan, pink, yellow, etc.: ""","""%prog -m mapping.txt -k white -o prefs_out_white.txt"""))
script_info['script_usage'].append(("""""","""If the user would like to change the monte_carlo distances, they can pass the '-d' option as follows: ""","""%prog -m mapping.txt -d 15 -o prefs_out_d15.txt"""))
script_info['script_usage'].append(("""""","""If the user would like to add a list of taxons they can pass the '-i' option, which is the resulting taxa file from summarize_taxa.py, as follows: ""","""%prog -m mapping.txt -i taxa_level_3.txt -o prefs_out_taxa_l3.txt"""))
script_info['script_usage'].append(("""""","""If the user would like to add the ball size scale they can pass the '-s' option as follows: ""","""%prog -m mapping.txt -s 3 -o prefs_out_s3.txt"""))
script_info['script_usage'].append(("""""","""If the user would like to add the head and line color for the arrows in the procrustes analysis plot they can pass the '-a' and '-l' options as follows: ""","""%prog -m mapping.txt -a black -l blue -o prefs_out_procrustes.txt"""))

script_info['output_description']="""The result of this script is a text file, containing coloring preferences to be used by make_distance_histograms.py, make_2d_plots.py and make_3d_plots.py."""
script_info['optional_options']=[]


script_info['required_options']=[\
    make_option('-m', '--map_fname', dest='map_fname', type='existing_filepath',\
     help='This is the metadata mapping file [default=%default]'),
    options_lookup['output_fp']
]

script_info['optional_options']=[\
    make_option('-b','--mapping_headers_to_use',action='store',\
          type='string',dest='mapping_headers_to_use',help='mapping fields to '+\
          'use in prefs file [default: %default]', default='ALL'),\
    make_option('-k', '--background_color',type='string',help='This is the background'+ \
          'color to  use in the plots. [default: %default]',default='black'),
    make_option('-d','--monte_carlo_dists',action='store',\
          type='string',dest='monte_carlo_dist',help='monte carlo distance'+\
          'to use for each sample header [default: %default]',default=10),\
    make_option('-i', '--input_taxa_file', dest='input_taxa_file',\
      action='store',type='existing_filepath', help='summarized taxa file with sample' + \
            'counts by taxonomy (resulting file from summarize_taxa.py)'),\
    make_option('-s', '--ball_scale', type='float',\
      help='scale factor for the size of each ball in the plots' + \
      ' [default: %default]', default=1.0),\
    make_option('-l', '--arrow_line_color',type='string', help='arrow line color for' + \
            'procrustes analysis. [default: %default]', default='white'),
    make_option('-a', '--arrow_head_color', type='string', help='arrow head color for' + \
            'procrustes analysis. [default: %default]', default='red'),
]

script_info['version']=__version__

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)
    
    data={}
    mapping,headers,comments = get_map(opts, data)
    
    mapping_headers_to_use=opts.mapping_headers_to_use
    background_color=opts.background_color
    monte_carlo_dist=opts.monte_carlo_dist
    ball_scale=opts.ball_scale
    arrow_line_color=opts.arrow_line_color
    arrow_head_color=opts.arrow_head_color
    
    taxonomy_count_file = opts.input_taxa_file
    
    if taxonomy_count_file:
        try:
            counts_f = open(taxonomy_count_file, 'U').readlines()
            _, taxa_ids, _ = \
                       parse_taxa_summary_table(counts_f)
        except (TypeError, IOError):
            raise ValueError, 'Summarized taxa file could not be parsed.'
    else:
        taxa_ids=None
        
    out = build_prefs_string(mapping_headers_to_use, background_color, \
                                monte_carlo_dist, headers, taxa_ids, \
                                ball_scale, arrow_line_color, arrow_head_color)
                                
    f = open(opts.output_fp,'w')
    f.write(out)
    f.close()

if __name__ == "__main__":
    main()