CODEWITHSUNDEEP
perlcommand-linesystem
CiaranWelsh
CiaranWelsh

Reputation: 7681

Using optional arguments from command line within the system function in perl

I am generalizing a pre-existing perl script... i.e. making it work on numerous instances simultaneously. Basically it is a parameter scan feature of a modelling script. The scan does a single parameter and I want it to do them all. The pre-existing script (called scan_var.pl from bionetgen if your interested) has a bunch of arguments - some of them optional.

The following is successful in implementing the parameter scan with the default settings 

#execute the parameter scan with each variable individually

foreach $var_name (@var_names){

    my $param = shift @var_names;
    system ("perl", $scan_var_location, $model, $param, $min_value, $max_value, $NPTS);
}

But now I want to use the GetOpt::Long module to parse in the optional arguments. My code so far is: 

# some default parameters
my $log     = 0;
my $t_end   = 20;
my $n_steps = 1;
my $steady_state = 0;
my $method = "\"ode\"";
my $verbose = 0;
my $prefix;

my $options = GetOptions ( 
                           'verbose'      => \$verbose, #boolean
                           'log'          => \$log, #boolean
                           'n_steps:i'    => \$n_steps, #integer
                           'steady_state' => \$steady_state, #boolean
                           'method:s'     => \$method, #string
                           't_end:i'      => \$t_end, #integer
                           'prefix:s'     => \$prefix string
                         );

#execute the parameter scan with each variable individually

foreach $var_name (@var_names){ #iterates through a list stored in $var_names(not shown for concise-ness)

    my $param = shift @var_names;

    system ("perl", $scan_var_location, #required value, directory
                    $options, #optional command line arguments - corresponds to the list above
                    $model, #required command line value (directory)
                    $param, #list iterated over
                    $min_value, #requierd integer
                    $max_value, #required integer
                    $NPTS #required integer
           );
}

This however is somehow incorrect. Does anybody have any suggestions for corrections?

Cheers

Upvotes: 0

Views: 1004

Answers (3)

Miller
Miller

Reputation: 35208

The following is a tighter version of your code:

GetOptions ( 
    'verbose'      => \(my $verbose = 0),        #boolean
    'log'          => \(my $log     = 0),        #boolean
    'n_steps:i'    => \(my $n_steps = 1),        #integer
    'steady_state' => \(my $steady_state = 0),   #boolean
    'method:s'     => \(my $method = q{"ode"}),  #string
    't_end:i'      => \(my $t_end   = 20),       #integer
    'prefix:s'     => \my $prefix,               #string
);

#execute the parameter scan with each variable individually

#iterates through a list stored in $var_names(not shown for concise-ness)
foreach $var_name (@var_names) { 
    system("perl", 
        $scan_var_location,   #required value, directory
        $model,               #required command line value (directory)
        $var_name,            #list iterated over
        $min_value,           #requierd integer
        $max_value,           #required integer
        $NPTS,                #required integer
    );
}

Upvotes: 0

Zaid
Zaid

Reputation: 37146

GetOptions() supports the storage of values in a hash. This allows you to reduce variable clutter:

use Getopt::Long;

my %options;
GetOptions( \%options,
                       'verbose',
                           'log',
                     'n_steps:i',
                  'steady_state',
                      'method:s',
                       't_end:i',
                      'prefix:s',
          );

my $stringified_options = join ' ', map "-$_ $options{$_}", keys %options;

foreach my $var_name ( @var_name ) {

    system ("perl", $scan_var_location,
                    $stringified_options,
                    $model,
                    $param, 
                    $min_value,
                    $max_value,
                    $NPTS
           );
}

Upvotes: 1

toolic
toolic

Reputation: 62154

One problem is that you probably don't want to use the return value of GetOptions in your system call. $options has the return value:

GetOptions returns true to indicate success. It returns false when the function detected one or more errors during option parsing.

Upvotes: 0

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