new module for facilitating script authors to fetch db-related arguments

modules/Bio/EnsEMBL/Utils/EasyArgv.pm

+#
+
+=head1 NAME
+
+Bio::EnsEMBL::Utils::EasyArgv
+
+=head1 SYNOPSIS
+
+    use Bio::EnsEMBL::Utils::EasyArgv;
+    my $db = get_ens_db_from_argv; # this method is exported.
+    use Getopt::Long;
+    my ($others);
+    &GetOptions(
+        'others=s' => \$others
+    );
+
+=head1 DESCRIPTION
+
+This is a lazy but easy way to get the db-related arguments. All you need to do
+is to invoke get_ens_db_from_argv before using standard Getopt. The below 
+options will be absorbed and removed from @ARGV.
+
+db_file, host, db_host, dbhost, user, db_user, dbuser, pass, db_pass, dbpass,
+dbname, db_name.
+
+Now you can take advantage of Perl's do method to execute a file as perl script and get returned the last line of it. For your most accessed db setting, you 
+can have a file named, say, ensdb_homo_core_18.perlobj, with the content like
+
+    use strict;  # The ceiling line
+    use Bio:: EnsEMBL::DBSQL::DBAdaptor;
+    my $db = Bio:: EnsEMBL::DBSQL::DBAdaptor->new(
+        -host => 'ensembldb.ensembl.org',
+        -user => 'anonymous',
+        -dbname => 'homo_sapiens_core_18_34'
+        );
+    $db;  # The floor line
+
+In the your command line, you just need to write like 
+
+perl my_script.pl -db_file ensdb_homo_core_18.perlobj
+
+rather than verbose 
+
+-host ensembldb.ensembl.org -user anonymous -dbname homo_sapiens_core_18_34
+
+
+=head1 AUTHOR
+
+Juguang XIAO, juguang@tll.org.sg
+
+Other contributors' names here.
+
+=cut
+
+use strict;
+
+package Bio::EnsEMBL::Utils::EasyArgv;
+use vars qw(@ISA @EXPORT);
+use vars qw($debug);
+use Exporter ();
+@ISA= qw(Exporter);
+@EXPORT = qw(get_ens_db_from_argv
+);
+use Bio::Root::Root; # For _load_module
+use Getopt::Long;
+
+sub _debug_print;
+
+sub get_ens_db_from_argv {
+    my ($db_file, $host, $user, $pass, $dbname, $db_module);
+    $host = 'localhost';
+    $db_module = 'Bio::EnsEMBL::SQL::DBAdaptor';
+    Getopt::Long::config('pass_through');
+    &GetOptions(
+        'db_file=s' => \$db_file,
+        'host|dbhost|db_host=s' => \$host,
+        'user|dbuser|db_user=s' => \$user,
+        'pass|dbpass|db_pass=s' => \$pass,
+        'dbname|db_name=s' => \$dbname,
+        'db_module=s' => \$db_module
+    );
+
+    my $db;
+    if(defined $db_file){
+        -e $db_file or die "'$db_file' is defined but does not exist\n";
+        eval { $db = do($db_file) };
+        $@ and die "'$db_file' is not a perlobj file\n";
+        $db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')
+            or die "'$db_file' is not EnsEMBL DBAdaptor\n";
+        _debug_print "I get a db from file\n";
+        
+    }elsif(defined $host && defined $user && defined $dbname){
+        Bio::Root::Root::_load_module($db_module);
+        $db = $db_module->new(
+            -host => $host,
+            -user => $user,
+            -pass => $pass,
+            -dbname => $dbname
+        );
+    }else{
+        die "Cannot get the db, due to the insufficient information\n";
+    }
+    return $db;
+}
+
+sub _debug_print {
+    print STDERR @_ if $debug;
+}
+
+
+1;

modules/t/easyargv.t

+use strict;
+use lib 't';
+use Test;
+
+BEGIN { $| = 1; plan tests => 1;}
+
+use Bio::EnsEMBL::Utils::EasyArgv;
+ok(1);
+
+my @argv = @ARGV;
+
+