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utils/runDiscovery.pl  view on Meta::CPAN

# CONSTANT STRINGS
###############################################################################

my $usage = "Error Running LBD, Usage Instructions:\n\n"
."   runDiscovery LBD_CONFIG_FILE [OPTIONS]\n\n"
."FLAGS\n"
."   --debug       Print EVERYTHING to STDERR.\n"
."   --help        Print this help screen.\n"
."   --version     Print the version number\n"
."\nOPTIONS\n"
."   --assocConfig        path to the UMLS::Association Config File\n"
."   --interfaceConfig    path to the UMLS::Interface Config File\n"
."\nUSAGE EXAMPLES\n"
."   runDiscovery lbdConfigFile\n";
;

#############################################################################
#                       Parse command line options 
#############################################################################
my $DEBUG = 0;      # Prints EVERYTHING. Use with small testing files.        
my $HELP = '';      # Prints usage and exits if true.
my $VERSION;

#set default param values
my %options = ();
$options{'assocConfig'}  = '';
$options{'interfaceConfig'} = '';

#grab all the options and set values
GetOptions( 'debug'             => \$DEBUG, 
            'help'              => \$HELP,
	    'version'           => \$VERSION,
            'assocConfig=s'     => \$options{'assocConfig'},
            'interfaceConfig=s' => \$options{'interfaceConfig'},
);
 
#Check for version or help
if ($VERSION) {
    print "current version is ".(ALBD->version())."\n";
    exit;
}     
if ($HELP) {
    &showHelp();
    exit;
}    


############################################################################
#                          Begin Running LBD
############################################################################

$options{'lbdConfig'} = shift;
defined $options{'lbdConfig'} or die ($usage);

my $lbd = ALBD->new(\%options);
$lbd->performLBD();

############################################################################
#  function to output help messages for this program
############################################################################
sub showHelp() {
        
    print "This utility takes an lbd configuration file and outputs\n";
    print "the results of lbd to file. The parameters for LBD are\n";
    print "specified in the input file. Please see samples/lbd or\n";
    print "samples/thresholding for sample input files and descriptions\n";
    print "of parameters and full details on what can be in an LBD input\n";
    print "file.\n";
    
    print "\n";
    print "Usage: runDiscovery.pl LBD_CONFIG_FILE [OPTIONS]\n";
    
    print "\n";
    print "General Options:\n\n";
    print "--help               displays help, a quick summary of program\n"; 
    print "                     options\n";
    print "--assocConfig        path to a UMLS::Association configuration\n";
    print "                     file. Default location is \n";
    print "                     '../config/association'. Replace this file\n";
    print "                     for your computer to avoid having to specify\n";
    print "                     each time.\n";
    print "--interfaceConfig    path to a UMLS::Interface configuration\n";
    print "                     file. Default location is \n";
    print "                     '../config/interface'. Replace this file \n";
    print "                     for your computer to avoid having to specify\n";
    print "                     each time.\n";
    print "--debug              enter debug mode\n";
    print "--version            prints the current version to screen\n";
};