branch-1-6/Bio/DB/Ace.pm

   1
   2 # $Id$
   3 #
   4 # BioPerl module for Bio::DB::Ace
   5 #
   6 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   7 #
   8 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   9 #
  10 # Copyright Ewan Birney
  11 #
  12 # You may distribute this module under the same terms as perl itself
  13
  14 # POD documentation - main docs before the code
  15
  16 =head1 NAME
  17
  18 Bio::DB::Ace - Database object interface to ACeDB servers
  19
  20 =head1 SYNOPSIS
  21
  22     $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
  23
  24     $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
  25
  26     # or ...
  27
  28     $seq = $db->get_Seq_by_acc('J00522'); # Accession Number
  29
  30 =head1 DESCRIPTION
  31
  32 This provides a standard BioPerl database access to Ace, using Lincoln Steins
  33 excellent AcePerl module. You need to download and install the aceperl module from
  34
  35   http://stein.cshl.org/AcePerl/
  36
  37 before this interface will work.
  38
  39 This interface is designed at the moment to work through a aceclient/aceserver
  40 type mechanism
  41
  42 =head1 INSTALLING ACEPERL
  43
  44 Download the latest aceperl tar file, gunzip/untar and cd into the directory.
  45 This is a standard CPAN-style directory, so if you go
  46
  47   Perl Makefile.PL
  48   make
  49   <become root>
  50   make install
  51
  52 Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
  53
  54 =head1 FEEDBACK
  55
  56 =head2 Mailing Lists
  57
  58 User feedback is an integral part of the evolution of this
  59 and other Bioperl modules. Send your comments and suggestions preferably
  60  to one of the Bioperl mailing lists.
  61 Your participation is much appreciated.
  62
  63   bioperl-l@bioperl.org                  - General discussion
  64   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  65
  66 =head2 Support
  67
  68 Please direct usage questions or support issues to the mailing list:
  69
  70 I<bioperl-l@bioperl.org>
  71
  72 rather than to the module maintainer directly. Many experienced and
  73 reponsive experts will be able look at the problem and quickly
  74 address it. Please include a thorough description of the problem
  75 with code and data examples if at all possible.
  76
  77 =head2 Reporting Bugs
  78
  79 Report bugs to the Bioperl bug tracking system to help us keep track
  80 the bugs and their resolution.  Bug reports can be submitted via the
  81 web:
  82
  83   http://bugzilla.open-bio.org/
  84
  85 =head1 AUTHOR - Ewan Birney
  86
  87 Email birney@ebi.ac.uk
  88
  89 =head1 APPENDIX
  90
  91 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  92
  93 =cut
  94
  95 # Let the code begin...
  96
  97 package Bio::DB::Ace;
  98 use strict;
  99
 100 # Object preamble - inherits from Bio::DB::RandomAccessI
 101
 102 use Bio::Seq;
 103
 104 BEGIN {
 105   eval "require Ace;";
 106   if( $@) {
 107     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 $@";
 108   }
 109 }
 110
 111
 112 use base qw(Bio::DB::RandomAccessI);
 113
 114 # new() is inherited from Bio::DB::Abstract
 115
 116 # _initialize is where the heavy stuff will happen when new is called
 117
 118 sub new {
 119   my($class,@args) = @_;
 120   my $self = $class->SUPER::new(@args);
 121   my ($host,$port) = $self->_rearrange([qw(
 122                                          HOST
 123                                          PORT
 124                                          )],
 125                                      @args,
 126                                      );
 127
 128   if( !$host || !$port ) {
 129     $self->throw("Must have a host and port for an acedb server to work");
 130   }
 131
 132   my $aceobj = Ace->connect(-host => $host,
 133                             -port => $port) ||
 134                               $self->throw("Could not make acedb object to $host:$port");
 135
 136   $self->_aceobj($aceobj);
 137
 138
 139   return $self;
 140 }
 141
 142 =head2 get_Seq_by_id
 143
 144  Title   : get_Seq_by_id
 145  Usage   : $seq = $db->get_Seq_by_id($uid);
 146  Function: Gets a Bio::Seq object by its unique identifier/name
 147  Returns : a Bio::Seq object
 148  Args    : $id : the id (as a string) of the desired sequence entry
 149
 150 =cut
 151
 152 sub get_Seq_by_id {
 153   my $self = shift;
 154   my $id = shift or $self->throw("Must supply an identifier!\n");
 155   my $ace = $self->_aceobj();
 156   my ($seq,$dna,$out);
 157
 158   $seq = $ace->fetch( 'Sequence' , $id);
 159
 160   # get out the sequence somehow!
 161
 162   $dna = $seq->asDNA();
 163
 164   $dna =~ s/^>.*\n//;
 165   $dna =~ s/\n//g;
 166
 167   $out = Bio::Seq->new( -id => $id, -alphabet => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
 168   return $out;
 169
 170 }
 171
 172 =head2 get_Seq_by_acc
 173
 174   Title   : get_Seq_by_acc
 175   Usage   : $seq = $db->get_Seq_by_acc($acc);
 176   Function: Gets a Bio::Seq object by its accession number
 177   Returns : a Bio::Seq object
 178   Args    : $acc : the accession number of the desired sequence entry
 179
 180
 181 =cut
 182
 183 sub get_Seq_by_acc {
 184
 185   my $self = shift;
 186   my $acc = shift or $self->throw("Must supply an accesion number!\n");
 187
 188   return $self->get_Seq_by_id($acc);
 189 }
 190
 191 =head2 _aceobj
 192
 193   Title   : _aceobj
 194   Usage   : $ace = $db->_aceobj();
 195   Function: Get/Set on the acedb object
 196   Returns : Ace object
 197   Args    : New value of the ace object
 198
 199 =cut
 200
 201 sub _aceobj {
 202   my ($self,$arg) = @_;
 203
 204   if( $arg ) {
 205     $self->{'_aceobj'} = $arg;
 206   }
 207
 208   return $self->{'_aceobj'};
 209 }
 210
 211 1;
 212
 213
 214
 215
 216
 217