Bio/DB/Ace.pm

   1
   2 #
   3 # BioPerl module for Bio::DB::Ace
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   8 #
   9 # Copyright Ewan Birney
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::DB::Ace - Database object interface to ACeDB servers
  18
  19 =head1 SYNOPSIS
  20
  21     $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
  22
  23     $seq = $db->get_Seq_by_id('J00522'); # Unique ID
  24
  25     # or ...
  26
  27     $seq = $db->get_Seq_by_acc('J00522'); # Accession Number
  28
  29 =head1 DESCRIPTION
  30
  31 This provides a standard BioPerl database access to Ace, using Lincoln Steins
  32 excellent AcePerl module. You need to download and install the aceperl module from
  33
  34   http://stein.cshl.org/AcePerl/
  35
  36 before this interface will work.
  37
  38 This interface is designed at the moment to work through a aceclient/aceserver
  39 type mechanism
  40
  41 =head1 INSTALLING ACEPERL
  42
  43 Download the latest aceperl tar file, gunzip/untar and cd into the directory.
  44 This is a standard CPAN-style directory, so if you go
  45
  46   Perl Makefile.PL
  47   make
  48   <become root>
  49   make install
  50
  51 Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
  52
  53 =head1 FEEDBACK
  54
  55 =head2 Mailing Lists
  56
  57 User feedback is an integral part of the evolution of this
  58 and other Bioperl modules. Send your comments and suggestions preferably
  59  to one of the Bioperl mailing lists.
  60 Your participation is much appreciated.
  61
  62   bioperl-l@bioperl.org                  - General discussion
  63   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  64
  65 =head2 Support
  66
  67 Please direct usage questions or support issues to the mailing list:
  68
  69 I<bioperl-l@bioperl.org>
  70
  71 rather than to the module maintainer directly. Many experienced and
  72 reponsive experts will be able look at the problem and quickly
  73 address it. Please include a thorough description of the problem
  74 with code and data examples if at all possible.
  75
  76 =head2 Reporting Bugs
  77
  78 Report bugs to the Bioperl bug tracking system to help us keep track
  79 the bugs and their resolution.  Bug reports can be submitted via the
  80 web:
  81
  82   https://redmine.open-bio.org/projects/bioperl/
  83
  84 =head1 AUTHOR - Ewan Birney
  85
  86 Email birney@ebi.ac.uk
  87
  88 =head1 APPENDIX
  89
  90 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  91
  92 =cut
  93
  94 # Let the code begin...
  95
  96 package Bio::DB::Ace;
  97 use strict;
  98
  99 # Object preamble - inherits from Bio::DB::RandomAccessI
 100
 101 use Bio::Seq;
 102
 103 BEGIN {
 104   eval "require Ace;";
 105   if( $@) {
 106     print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@";
 107   }
 108 }
 109
 110
 111 use base qw(Bio::DB::RandomAccessI);
 112
 113 # new() is inherited from Bio::DB::Abstract
 114
 115 # _initialize is where the heavy stuff will happen when new is called
 116
 117 sub new {
 118   my($class,@args) = @_;
 119   my $self = $class->SUPER::new(@args);
 120   my ($host,$port) = $self->_rearrange([qw(
 121                                          HOST
 122                                          PORT
 123                                          )],
 124                                      @args,
 125                                      );
 126
 127   if( !$host || !$port ) {
 128     $self->throw("Must have a host and port for an acedb server to work");
 129   }
 130
 131   my $aceobj = Ace->connect(-host => $host,
 132                             -port => $port) ||
 133                               $self->throw("Could not make acedb object to $host:$port");
 134
 135   $self->_aceobj($aceobj);
 136
 137
 138   return $self;
 139 }
 140
 141 =head2 get_Seq_by_id
 142
 143  Title   : get_Seq_by_id
 144  Usage   : $seq = $db->get_Seq_by_id($uid);
 145  Function: Gets a Bio::Seq object by its unique identifier/name
 146  Returns : a Bio::Seq object
 147  Args    : $id : the id (as a string) of the desired sequence entry
 148
 149 =cut
 150
 151 sub get_Seq_by_id {
 152   my $self = shift;
 153   my $id = shift or $self->throw("Must supply an identifier!\n");
 154   my $ace = $self->_aceobj();
 155   my ($seq,$dna,$out);
 156
 157   $seq = $ace->fetch( 'Sequence' , $id);
 158
 159   # get out the sequence somehow!
 160
 161   $dna = $seq->asDNA();
 162
 163   $dna =~ s/^>.*\n//;
 164   $dna =~ s/\n//g;
 165
 166   $out = Bio::Seq->new( -id => $id, -alphabet => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
 167   return $out;
 168
 169 }
 170
 171 =head2 get_Seq_by_acc
 172
 173   Title   : get_Seq_by_acc
 174   Usage   : $seq = $db->get_Seq_by_acc($acc);
 175   Function: Gets a Bio::Seq object by its accession number
 176   Returns : a Bio::Seq object
 177   Args    : $acc : the accession number of the desired sequence entry
 178
 179
 180 =cut
 181
 182 sub get_Seq_by_acc {
 183
 184   my $self = shift;
 185   my $acc = shift or $self->throw("Must supply an accession number!\n");
 186
 187   return $self->get_Seq_by_id($acc);
 188 }
 189
 190 =head2 _aceobj
 191
 192   Title   : _aceobj
 193   Usage   : $ace = $db->_aceobj();
 194   Function: Get/Set on the acedb object
 195   Returns : Ace object
 196   Args    : New value of the ace object
 197
 198 =cut
 199
 200 sub _aceobj {
 201   my ($self,$arg) = @_;
 202
 203   if( $arg ) {
 204     $self->{'_aceobj'} = $arg;
 205   }
 206
 207   return $self->{'_aceobj'};
 208 }
 209
 210 1;