LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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AUTHOR

Juguang Xiao <juguang@tll.org.sg>

NAME

Bio::EnsEMBL::Utils::EasyArgv

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 );

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

METHODS