Bio/DB/BioSQL/OBDA.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::DB::BioSQL::OBDA
   4 #
   5 # Copyright Brian Osborne
   6 #
   7 # You may distribute this module under the same terms as perl itself
   8
   9 # POD documentation - main docs before the code
  10
  11 =head1 NAME
  12
  13 Bio::DB::BioSQL::OBDA
  14
  15 =head1 SYNOPSIS
  16
  17 This module is meant to be used a part of the OBDA system, e.g.:
  18
  19   use Bio::DB::Registry;
  20
  21   my $registry = Bio::DB::Registry->new;
  22   my $db = $registry->get_database('biosql');
  23   my $seq = $db->get_Seq_by_acc('P41932');
  24
  25 =head1 DESCRIPTION
  26
  27 This module connects code that uses OBDA to the bioperl-db package
  28 and the underlying BioSQL database.
  29
  30 The Open Biological Database Access (OBDA) system was designed so that one
  31 could use the same application code to access data from multiple database
  32 types by simply changing a few lines in a configuration file. See
  33 L<http://www.bioperl.org/wiki/HOWTO:OBDA> for more information.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this
  40 and other Bioperl modules. Send your comments and suggestions preferably
  41 to one of the Bioperl mailing lists.
  42 Your participation is much appreciated.
  43
  44   bioperl-l@bio.perl.org
  45
  46 =head2 Reporting Bugs
  47
  48 Report bugs to the Bioperl bug tracking system to help us keep track
  49 the bugs and their resolution. Bug reports can be submitted via the web:
  50
  51   http://bugzilla.open-bio.org
  52
  53 =head1 AUTHOR - Brian Osborne
  54
  55 Email bosborne at alum.mit.edu
  56
  57 =head1 APPENDIX
  58
  59 The rest of the documentation details each of the object methods. Internal
  60 methods are usually preceded with a _
  61
  62 =cut
  63
  64 # Let the code begin...
  65
  66 package Bio::DB::BioSQL::OBDA;
  67 use strict;
  68 use Bio::DB::Query::BioQuery;
  69 use Bio::DB::BioDB;
  70 use base qw(Bio::Root::Root Bio::DB::RandomAccessI);
  71
  72 =head2 new_from_registry
  73
  74  Title   : new_from_registry
  75  Usage   :
  76  Function: Create a database object that can be used by OBDA
  77  Returns :
  78  Args    : Hash containing connection parameters read from an OBDA
  79            registry file
  80
  81 =cut
  82
  83 sub new_from_registry {
  84    my ($class, %conf) = @_;
  85         my $self = $class->SUPER::new();
  86         my ($host,$port);
  87         #  prevent warning msg by allowing location to be undef for postgresql 'ident sameuser' login)
  88         if (defined $conf{'location'}) {
  89                 ($host,$port) = split ":", $conf{'location'};
  90         }
  91         my $db = Bio::DB::BioDB->new( -database => 'biosql',
  92                                                                                   -host     => $host,
  93                                                                                   -port     => $port,
  94                                                                                   -dbname   => $conf{'dbname'},
  95                                                                                   -driver   => $conf{'driver'},
  96                                       -user     => $conf{'user'  },
  97                                                                                   -pass     => $conf{'passwd'} );
  98         $self->_db($db);
  99         $self;
 100 }
 101
 102 =head1 Methods inherited from Bio::DB::RandomAccessI
 103
 104 =head2 get_Seq_by_id
 105
 106  Title   : get_Seq_by_id
 107  Usage   : $seq = $db->get_Seq_by_id(12345)
 108  Function:
 109  Example :
 110  Returns : One or more Sequence objects
 111  Args    : An identifier
 112
 113 =cut
 114
 115 sub get_Seq_by_id {
 116    my ($self,$id) = @_;
 117         my $db = $self->_db;
 118         my @seqs = ();
 119         $self->throw("No identifier given") unless $id;
 120
 121         my $query = Bio::DB::Query::BioQuery->new(
 122                   -datacollections => ['Bio::SeqI seq'],
 123              -where => ["seq.primary_id = $id"]);
 124
 125         my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
 126         my $result = $seq_adaptor->find_by_query($query);
 127
 128         for my $seq ($result->next_object) {
 129                 push @seqs,$seq;
 130         }
 131         return wantarray ? @seqs : $seqs[0];
 132 }
 133
 134 =head2 get_Seq_by_acc
 135
 136  Title   : get_Seq_by_acc
 137  Usage   : $seq = $db->get_Seq_by_acc('A12345')
 138  Function:
 139  Example :
 140  Returns : One or more Sequence objects
 141  Args    : An accession number
 142
 143 =cut
 144
 145 sub get_Seq_by_acc {
 146    my ($self,$acc) = @_;
 147         my $db = $self->_db;
 148         my @seqs = ();
 149         $self->throw("No accession given") unless $acc;
 150
 151         my $query = Bio::DB::Query::BioQuery->new(
 152      -datacollections => ['Bio::SeqI seq'],
 153           -where => ["seq.accession_number = '$acc'"]);
 154
 155         my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
 156         my $result = $seq_adaptor->find_by_query($query);
 157
 158         for my $seq ($result->next_object) {
 159                 push @seqs,$seq;
 160         }
 161         return wantarray ? @seqs : $seqs[0];
 162 }
 163
 164 =head2 get_Seq_by_version
 165
 166  Title   : get_Seq_by_version
 167  Usage   : $seq = $db->get_Seq_by_version('A12345.3')
 168  Function:
 169  Example :
 170  Returns : One or more Sequence objects
 171  Args    : A versioned accession number
 172
 173 =cut
 174
 175 sub get_Seq_by_version {
 176    my ($self,$vacc) = @_;
 177         my $db = $self->_db;
 178         my @seqs = ();
 179         my ($acc,$ver) = split /\./, $vacc; # split on period
 180         $self->throw("Must supply a versioned accession: <accession>.<version>")
 181           unless ($acc && $ver);
 182
 183         my $query = Bio::DB::Query::BioQuery->new(
 184      -datacollections => ['Bio::SeqI seq'],
 185           -where => ["seq.accession_number = '$acc'",
 186                                          "seq.version = $ver"]);
 187
 188         my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
 189         my $result = $seq_adaptor->find_by_query($query);
 190
 191         for my $seq ($result->next_object) {
 192                 push @seqs,$seq;
 193         }
 194         return wantarray ? @seqs : $seqs[0];
 195 }
 196
 197 =head1 Private methods
 198
 199 =head2 _db
 200
 201  Title   : _db
 202  Usage   :
 203  Function: Get or set the BioDB object
 204  Example :
 205  Returns :
 206  Args    :
 207
 208 =cut
 209
 210 sub _db {
 211         my ($self,$db) = @_;
 212         $self->{_db} = $db if ($db);
 213         $self->{_db};
 214 }
 215
 216 1;
 217
 218 __END__