madM has asked for the wisdom of the Perl Monks concerning the following question:

Hi all,

im starting a script with the command line using getopt::long. I declare the array aminos at the first of the script and a subroutine should use the declared @aminos when i call it with the option sub but when i call the subroutine... the array @aminos is empty in the subroutine.. if i print @aminos in the suroutine it prints 0... do you know why is this happening and how i can prevent this from happening? 
GetOptions ( 'sub' => \&a
                  ) 

@aminos= qw (A R N D C Q E G H I L K M F P S T W Y V B Z X);

sub a {

if( "$substr1$substr2" =~ /[^@aminos]/ ) {
print "hello\n";
}

print "@aminos\n";

}

[download]

Replies are listed 'Best First'.
Re: array empty when calling script with getopt::long
by graff (Chancellor) on Apr 29, 2014 at 01:51 UTC
    Would it be too difficult or complicated for you to explain what sort of option processing you are actually hoping to do? Normally, when someone writes a command-line tool that handles optional args, it will print a synopsis whenever the user types a bad arg, or specifically asks for help.

    Usually, the programmer includes a "-h" option for displaying the synopsis, or simply lets Getopt::Long throw an error when "-h" or "-?" is used as an option, and makes sure to display the synopsis whenever Getopt::Long throws an error.

    What would the synopsis be for your script? Why would you need a subroutine to process your options? What do "$substr1" and "$substr2" contain (where is the code that assigns values to those variables)?

[reply]
Re: array empty when calling script with getopt::long
by Anonymous Monk on Apr 29, 2014 at 03:57 UTC

    In addition to what has been said, you could make the array variable "aminos" global, so that it can be accessed by all. But it's better to make a variable available close to where it's are needed.

    Your values to your scalar variables maybe gotten from the CLI and checked if initialized.

    Modifying your post a bit like this works, but you might still have to work on it or incorporate it with your code. 

    use warnings;
use strict;
use Getopt::Long qw(:config gnu_getopt);

help() if $ARGV[0] !~ /^--/;

my @aminos = qw (A R N D C Q E G H I L K M F P S T W Y V B Z X);

GetOptions(
    'substr1=s' => \my $substr1,
    'substr2=s' => \my $substr2,
    'sub'       => \&a,
    'help|?'    => \&help,
);

sub a {

    if ( "$substr1$substr2" =~ /[^@aminos]/ ) {
        print "hello\n";
    }

    print "@aminos\n";
}

sub help { print "Usage: script --substr1 value --substr2 value --sub"
+; exit }

    [download]
    You might have to check the usage of Getopt::Long again.

    Note, I didn't check for the initialization of substr1 and 2

[reply]
[d/l]
Re: array empty when calling script with getopt::long
by Laurent_R (Canon) on Apr 29, 2014 at 06:20 UTC
    Declaring and defining your @amino array before calling your GetOptions subroutine should be a remedy to your immediate problem. But, as already pointed out by other monks, there are a number of other issues in your code, including especially the fact that nobody knows what there is in the $substr1 and $substr2 variables, and that I do not understand what you are trying to achieve exactly with your pattern matching expression.
[reply]
Re: array empty when calling script with getopt::long
by LanX (Saint) on Apr 29, 2014 at 01:34 UTC
[reply]
      yes .. sorry for that... and thank you very much for your answer :)
[reply]

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