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1 #
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2 # Example of configuration file used by Bio::EnsEMBL::Registry::load_all
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3 # method to store/register all kind of Adaptors.
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4
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5 use strict;
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6 use warnings;
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7
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8 use Bio::EnsEMBL::Utils::ConfigRegistry;
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9 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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10 use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
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11
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12 my @aliases;
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13
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14 new Bio::EnsEMBL::DBSQL::DBAdaptor(
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15 '-host' => 'ensembldb.ensembl.org',
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16 '-user' => 'anonymous',
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17 '-port' => '3306',
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18 '-species' => 'Homo sapiens',
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19 '-group' => 'core',
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20 '-dbname' => 'homo_sapiens_core_23_34e'
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21 );
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22
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23 @aliases = ( 'H_Sapiens', 'homo sapiens',
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24 'Homo_Sapiens', 'Homo_sapiens',
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25 'Homo', 'homo',
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26 'human' );
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27
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28 Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
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29 '-species' => 'Homo sapiens',
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30 '-alias' => [@aliases] );
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31
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32 new Bio::EnsEMBL::DBSQL::DBAdaptor(
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33 '-host' => 'ensembldb.ensembl.org',
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34 '-user' => 'anonymous',
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35 '-port' => '3306',
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36 '-species' => 'Mus musculus',
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37 '-group' => 'core',
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38 '-dbname' => 'mus_musculus_core_23_32c'
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39 );
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40
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41 @aliases = ( 'M_Musculus', 'mus musculus',
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42 'Mus_Musculus', 'Mus_musculus',
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43 'Mus', 'mus',
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44 'mouse' );
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45
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46 Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
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47 '-species' => 'Mus musculus',
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48 '-alias' => [@aliases] );
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49
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50 new Bio::EnsEMBL::DBSQL::DBAdaptor(
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51 '-host' => 'ensembldb.ensembl.org',
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52 '-user' => 'anonymous',
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53 '-port' => '3306',
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54 '-species' => 'Rattus norvegicus',
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55 '-group' => 'core',
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56 '-dbname' => 'rattus_norvegicus_core_23_3c'
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57 );
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58
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59 @aliases = ( 'R_Norvegicus', 'rattus norvegicus',
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60 'Rattus_Norvegicus', 'Rattus_norvegicus',
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61 'Rattus', 'rattus',
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62 'rat' );
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63
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64 Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
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65 '-species' => 'Rattus norvegicus',
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66 '-alias' => [@aliases] );
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67
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68 new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
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69 '-host' => 'ensembldb.ensembl.org',
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70 '-user' => 'anonymous',
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71 '-port' => '3306',
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72 '-species' => 'Compara23',
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73 '-dbname' => 'ensembl_compara_23_1'
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74 );
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75
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76 @aliases = ( 'ensembl_compara_23_1', 'compara23' );
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77
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78 Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
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79 '-species' => 'Compara23',
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80 '-alias' => [@aliases]
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81 );
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82
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83 1;
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