If you don't mind introducing Moose and its dependencies, then MooseX::Getopt is a good way of setting up command-line options (some of the features that I'm using here are documented in MooseX::Getopt::Meta::Attribute)
For example, in MyApp.pm
package MyApp;
use Moose;
with 'MooseX::Getopt';
has 'extension' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Str',
cmd_aliases => 'b',
documentation => 'Short description of extension'
);
has 'liste_snp' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Str',
cmd_aliases => 'l'
);
has 'min_snp_per_cds' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Bool',
cmd_aliases => 's',
default => 1
);
has 'liste_geno' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Str',
cmd_aliases => 'g'
);
has 'reference_cds_fasta' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Str',
cmd_aliases => 'r'
);
has 'prefixe' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Str',
cmd_aliases => 'p'
);
has 'min_read_classe' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Int',
cmd_aliases => 'mc',
default => 30
);
has 'max_read_per_cent_ambi' => (
traits => ['Getopt'],
is => 'rw',
isa => 'Num',
cmd_aliases => 'a',
default => 1
);
sub print_options {
my $self = shift;
my $bam = $self->extension // 'undefined';
my $liste_snp = $self->liste_snp // 'undefined';
my $min_snp_cds = $self->min_snp_per_cds // 'undefined';
my $list_geno = $self->liste_geno // 'undefined';
my $ref_cds = $self->reference_cds_fasta // 'undefined';
my $prefixe = $self->prefixe // 'undefined';
my $seuil_min_classe = $self->min_read_classe // 'undefined';
my $seuil_max_amb = $self->max_read_per_cent_ambi // 'undefined';
print "extension: $bam\n";
print "liste_snp: $liste_snp\n";
print "min_snp_per_cds: $min_snp_cds\n";
print "list_geno: $list_geno\n";
print "reference_cds_fasta: $ref_cds\n";
print "prefixe: $prefixe\n";
print "min_read_classe: $seuil_min_classe\n";
print "max_read_per_cent_ambi: $seuil_max_amb\n";
}
1;
Then in
runapp.pl,
#!/usr/bin/env perl
use MyApp;
my $app = MyApp->new_with_options();
$app->print_options;
# ... rest of the script here
exit;
Here are some examples of running the script...
The output of
runapp.pl is:
extension: undefined
liste_snp: undefined
min_snp_per_cds: 1
list_geno: undefined
reference_cds_fasta: undefined
prefixe: undefined
min_read_classe: 30
max_read_per_cent_ambi: 1
The output of
runapp.pl --extention myext --mc 40 is:
extension: myext
liste_snp: undefined
min_snp_per_cds: 1
list_geno: undefined
reference_cds_fasta: undefined
prefixe: undefined
min_read_classe: 40
max_read_per_cent_ambi: 1
The output of
runapp.pl -? is:
usage: runapp.pl [-?abghlprs] [long options...]
-h -? --usage --help Prints this usage informati
+on.
-b STR --extension STR Short description of extens
+ion
-l STR --liste_snp STR
-s --min_snp_per_cds
-g STR --liste_geno STR
-r STR --reference_cds_fasta STR
-p STR --prefixe STR
--mc INT --min_read_classe INT
-a NUM --max_read_per_cent_ambi NUM
