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# $Id: Ace.pm,v 1.9 2001/06/18 15:53:42 dag Exp $
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# BioPerl module for Bio::DB::Ace
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# Cared for by Ewan Birney <birney@sanger.ac.uk>
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# Copyright Ewan Birney
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# You may distribute this module under the same terms as perl itself
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# POD documentation - main docs before the code
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Bio::DB::Ace - Database object interface to ACeDB servers
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$db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
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$seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
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$seq = $db->get_Seq_by_acc('J00522'); # Accession Number
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This provides a standard BioPerl database access to Ace, using Lincoln Steins
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excellent AcePerl module. You need to download and install the aceperl module from
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http://stein.cshl.org/AcePerl/
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before this interface will work.
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This interface is designed at the moment to work through a aceclient/aceserver
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=head1 INSTALLING ACEPERL
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Download the latest aceperl tar file, gunzip/untar and cd into the directory.
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This is a standard CPAN-style directory, so if you go
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Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
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User feedback is an integral part of the evolution of this
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and other Bioperl modules. Send your comments and suggestions preferably
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to one of the Bioperl mailing lists.
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Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/MailList.shtml - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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the bugs and their resolution.
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Bug reports can be submitted via email or the web:
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bioperl-bugs@bio.perl.org
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http://bio.perl.org/bioperl-bugs/
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=head1 AUTHOR - Ewan Birney
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Email birney@sanger.ac.uk
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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# Let the code begin...
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# Object preamble - inherits from Bio::DB::RandomAccessI
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use Bio::DB::RandomAccessI;
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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 $@";
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@ISA = qw(Bio::DB::RandomAccessI);
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# new() is inherited from Bio::DB::Abstract
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# _initialize is where the heavy stuff will happen when new is called
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my($class,@args) = @_;
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my $self = $class->SUPER::new(@args);
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my ($host,$port) = $self->_rearrange([qw(
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if( !$host || !$port ) {
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$self->throw("Must have a host and port for an acedb server to work");
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my $aceobj = Ace->connect(-host => $host,
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$self->throw("Could not make acedb object to $host:$port");
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$self->_aceobj($aceobj);
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Title : get_Seq_by_id
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Usage : $seq = $db->get_Seq_by_id($uid);
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Function: Gets a Bio::Seq object by its unique identifier/name
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Returns : a Bio::Seq object
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Args : $id : the id (as a string) of the desired sequence entry
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my $id = shift or $self->throw("Must supply an identifier!\n");
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my $ace = $self->_aceobj();
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$seq = $ace->fetch( 'Sequence' , $id);
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# get out the sequence somehow!
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$dna = $seq->asDNA();
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$out = Bio::Seq->new( -id => $id, -type => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
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=head2 get_Seq_by_acc
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Title : get_Seq_by_acc
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Usage : $seq = $db->get_Seq_by_acc($acc);
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Function: Gets a Bio::Seq object by its accession number
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Returns : a Bio::Seq object
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Args : $acc : the accession number of the desired sequence entry
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my $acc = shift or $self->throw("Must supply an accesion number!\n");
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return $self->get_Seq_by_id($acc);
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Usage : $ace = $db->_aceobj();
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Function: Get/Set on the acedb object
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Args : New value of the ace object
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my ($self,$arg) = @_;
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$self->{'_aceobj'} = $arg;
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return $self->{'_aceobj'};
added
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Bio/DB/Ace.pm
