Source Code for Module bpm.cmdargs.graph

 1  ''' 
 2  'graph.py' sets up the command line arguments for the 'genecentric-bpms-graph' 
 3  program. 
 4  ''' 
 5  import argparse 
 6   
 7  import bpm 
 8  from bpm.cmdargs import assert_read_access 
 9   
10  parser = argparse.ArgumentParser( 
11      description='Graph BPMs', 
12      formatter_class=argparse.ArgumentDefaultsHelpFormatter) 
13  aa = parser.add_argument 
14  aa('geneinter', type=str, 
15     metavar='INPUT_GENETIC_INTERACTION_FILE', help='Location of the GI file.') 
16  aa('bpm', type=str, 
17     metavar='INPUT_BPM_FILE', help='Location of the BPM file to graph.') 
18  aa('output_dir', type=str, 
19     metavar='OUTPUT_DIRECTORY', help='Where the graph files will be written.') 
20  aa('-e', '--ignore-list', dest='ignore', type=str, default=None, 
21     metavar='IGNORE_FILE', 
22     help='The location of an ignore gene list file. (One gene per line.) ' 
23          'Any genes in this file will be excluded from the set of genes used ' 
24          'to generate BPMs.') 
25  aa('--no-squaring', dest='squaring', action='store_false', 
26     help='If set, genetic interaction scores will not be squared. ' 
27          'Squaring typically speeds convergence.') 
28  aa('-v', '--verbose', dest='verbose', action='store_true', 
29     help='If set, more output will be shown.') 
30   
31  conf = parser.parse_args() 
32   
33  # Set the global conf variable 
34  bpm.conf = conf 
35