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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =head1 AUTHOR
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20
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21 Juguang Xiao <juguang@tll.org.sg>
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22
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23 =cut
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24
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25 =head1 NAME
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26
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27 Bio::EnsEMBL::Utils::EasyArgv
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28
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29 =head1 SYNOPSIS
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30
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31 use Bio::EnsEMBL::Utils::EasyArgv;
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32
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33 my $db = get_ens_db_from_argv; # this method is exported.
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34
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35 use Getopt::Long;
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36
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37 my $others;
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38 &GetOptions( 'others=s' => \$others );
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39
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40 =head1 DESCRIPTION
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41
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42 This is a lazy but easy way to get the db-related arguments. All you
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43 need to do is to invoke get_ens_db_from_argv before using standard
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44 Getopt. The below options will be absorbed and removed from @ARGV.
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45
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46 db_file, host, db_host, dbhost, user, db_user, dbuser, pass, db_pass,
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47 dbpass, dbname, db_name.
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48
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49 Now you can take advantage of Perl's do method to execute a file as perl
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50 script and get returned the last line of it. For your most accessed db
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51 setting, you can have a file named, say, ensdb_homo_core_18.perlobj,
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52 with the content like
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53
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54 use strict; # The ceiling line
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55
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56 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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57
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58 my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
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59 -host => 'ensembldb.ensembl.org',
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60 -user => 'anonymous',
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61 -dbname => 'homo_sapiens_core_18_34'
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62 );
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63
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64 $db; # The floor line
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65
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66 In the your command line, you just need to write like
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67
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68 perl my_script.pl -db_file ensdb_homo_core_18.perlobj
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69
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70 rather than the verbose
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71
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72 -host ensembldb.ensembl.org -user anonymous \
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73 -dbname homo_sapiens_core_18_34
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74
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75 =head1 METHODS
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76
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77 =cut
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78
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79 package Bio::EnsEMBL::Utils::EasyArgv;
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80
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81 use strict;
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82 use vars qw($debug);
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83 use Exporter ();
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84 our @ISA= qw(Exporter);
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85 our @EXPORT = qw(get_ens_db_from_argv
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86 );
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87 use Bio::Root::Root; # For _load_module
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88 use Getopt::Long;
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89
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90 sub _debug_print;
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91
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92 sub get_ens_db_from_argv {
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93 my ($db_file, $host, $user, $pass, $dbname, $driver, $db_module);
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94 $host = 'localhost';
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95 $driver ='mysql';
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96 $db_module = 'Bio::EnsEMBL::SQL::DBAdaptor';
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97 Getopt::Long::config('pass_through');
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98 &GetOptions(
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99 'db_file=s' => \$db_file,
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100 'driver|dbdriver|db_driver=s' => \$driver,
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101 'host|dbhost|db_host=s' => \$host,
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102 'user|dbuser|db_user=s' => \$user,
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103 'pass|dbpass|db_pass=s' => \$pass,
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104 'dbname|db_name=s' => \$dbname,
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105 'db_module=s' => \$db_module
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106 );
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107
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108 my $db;
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109 if(defined $db_file){
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110 -e $db_file or die "'$db_file' is defined but does not exist\n";
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111 eval { $db = do($db_file) };
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112 $@ and die "'$db_file' is not a perlobj file\n";
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113 $db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')
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114 or die "'$db_file' is not EnsEMBL DBAdaptor\n";
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115 _debug_print "I get a db from file\n";
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116
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117 }elsif(defined $host and defined $user and defined $dbname){
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118 Bio::Root::Root::_load_module($db_module);
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119 $db = $db_module->new(
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120 -host => $host,
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121 -user => $user,
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122 -pass => $pass,
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123 -dbname => $dbname,
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124 -driver => $driver
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125 );
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126 }else{
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127 die "Cannot get the db, due to the insufficient information\n";
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128 }
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129 return $db;
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130 }
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131
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132 sub _debug_print {
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133 print STDERR @_ if $debug;
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134 }
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135
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136
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137 1;
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