Passing multiple file lists to perl script - perl

Question

I want to pass two file lists to my perl script and have them handled with Getopt::Long for storing an array (via a reference) in a dictionary.
#!/usr/bin/env perl
# author:sb2
use strict;
use warnings;
use Getopt::Long;
use File::Basename;
use Data::Dumper;
print Dumper(#ARGV);
my($config);
$config = &configure(scalar #ARGV);
sub configure{
my $args = shift;
my $config = {};
my #current_samples = ();
#my #old_samples = ();
$config = {'current_samples' => \#current_samples};
#$config = {'old_samples' => \#old_samples};
GetOptions($config,
#"old_samples=s{,}",
"current_samples=s{,}",
"help|h!", )
|| warn "error : $!\n";
print Dumper($config);
return($config);
}
I can happily pass one file list and have it stored as expected:
[sb2 ~]$ perl test.pl -current_samples WS*
$VAR1 = '-current_samples';
$VAR2 = 'WS68726_1401';
$VAR3 = 'WS68726_1402';
$VAR4 = 'WS68726_1500';
$VAR5 = 'WS68726_1501';
$VAR1 = {
'current_samples' => [
'WS68726_1401',
'WS68726_1402',
'WS68726_1500',
'WS68726_1501'
]
};
However, when I uncomment my second list parameter and use that my 'current_samples' variable is now a string with a single filename. Although the 'old_samples' variable has parsed correctly (as above):
[sb2 ~]$ perl test.pl -current_samples WS* -old_samples HG*
$VAR1 = '-current_samples';
$VAR2 = 'WS68726_1401';
$VAR3 = 'WS68726_1402';
$VAR4 = 'WS68726_1500';
$VAR5 = 'WS68726_1501';
$VAR6 = '-old_samples';
$VAR7 = 'HG001';
$VAR8 = 'HG002';
$VAR9 = 'HG003';
$VAR1 = {
'current_samples' => 'WS68726_1501'
'old_samples' => [
'HG001',
'HG002',
'HG003'
]
};
I tried swapping the order of variables around and the only one that made a difference was switching the config assignment ones:
sub configure{
my $args = shift;
my $config = {};
my #current_samples = ();
#my #old_samples = ();
$config = {'current_samples' => \#current_samples};
#$config = {'old_samples' => \#old_samples};
GetOptions($config,
"current_samples=s{,}",
"old_samples=s{,}",
"help|h!", )
|| warn "error : $!\n";
print Dumper($config);
return($config);
}
Produces:
[sb2 ~]$ perl test.pl -current_samples WS* -old_samples HG*
$VAR1 = '-current_samples';
$VAR2 = 'WS68726_1401';
$VAR3 = 'WS68726_1402';
$VAR4 = 'WS68726_1500';
$VAR5 = 'WS68726_1501';
$VAR6 = '-old_samples';
$VAR7 = 'HG001';
$VAR8 = 'HG002';
$VAR9 = 'HG003';
$VAR1 = {
'current_samples' => [
'WS68726_1401',
'WS68726_1402',
'WS68726_1500',
'WS68726_1501'
],
'old_samples' => 'HG003'
};
I can't see anything in the GetOptions CPAN page which alludes to this ordering affect so any help would be greatly appreciated!

Answer 1

From your commented code it looks like you are overwriting $config with these lines:
$config = {'current_samples' => \#current_samples};
#$config = {'old_samples' => \#old_samples};
Instead, do all config assignments in one line:
my $config = {
'current_samples' => \#current_samples,
'old_samples' => \#old_samples,
};
Or you can do them in single lines and assign to the keys of the hashref:
my $config = {};
$config->{'current_samples'} = \#current_samples;
$config->{'old_samples'} = \#old_samples;

Answer 2

As a an alternative solution, Getopt::Declare has syntax to support loading arguments into array references as well:
use strict;
use warnings;
use Getopt::Declare;
my $args = Getopt::Declare->new(
join( "\n",
'[strict]',
"-current-samples <files>... \t List of file names",
"-old-samples <files>... \t List of file names",
)
) || exit(1);
the ... after each tag tells Getopt::Declare to gather arguments into an array reference.
Then you just specify multiple space-separated values on the command line:
perl test-getopt-declare.pl -current-samples a b c d e f -old-samples 1 2 3 4 5 6