view variant_effect_predictor/Bio/EnsEMBL/Utils/EasyArgv.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=head1 AUTHOR

Juguang Xiao <[e-mail]>

=cut

=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 the verbose

  -host ensembldb.ensembl.org -user anonymous \
  -dbname homo_sapiens_core_18_34

=head1 METHODS

=cut

package Bio::EnsEMBL::Utils::EasyArgv;

use strict;
use vars qw($debug);
use Exporter ();
our @ISA= qw(Exporter);
our @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, $driver, $db_module);
    $host = 'localhost';
    $driver ='mysql';
    $db_module = 'Bio::EnsEMBL::SQL::DBAdaptor';
    Getopt::Long::config('pass_through');
    &GetOptions(
        'db_file=s' => \$db_file,
        'driver|dbdriver|db_driver=s' => \$driver,
        '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 and defined $user and defined $dbname){
        Bio::Root::Root::_load_module($db_module);
        $db = $db_module->new(
            -host => $host,
            -user => $user,
            -pass => $pass,
            -dbname => $dbname,
            -driver => $driver
        );
    }else{
        die "Cannot get the db, due to the insufficient information\n";
    }
    return $db;
}

sub _debug_print {
    print STDERR @_ if $debug;
}


1;