Bio::DB::Ace - Database object interface to ACeDB servers
$db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000'); $seq = $db->get_Seq_by_id('J00522'); # Unique ID # or ... $seq = $db->get_Seq_by_acc('J00522'); # Accession Number
This provides a standard BioPerl database access to Ace, using Lincoln Steins excellent AcePerl module. You need to download and install the aceperl module from
before this interface will work.
This interface is designed at the moment to work through a aceclient/aceserver type mechanism
Download the latest aceperl tar file, gunzip/untar and cd into the directory. This is a standard CPAN-style directory, so if you go
Perl Makefile.PL make <become root> make install
Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id($uid); Function: Gets a Bio::Seq object by its unique identifier/name Returns : a Bio::Seq object Args : $id : the id (as a string) of the desired sequence entry
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc($acc); Function: Gets a Bio::Seq object by its accession number Returns : a Bio::Seq object Args : $acc : the accession number of the desired sequence entry
Title : _aceobj Usage : $ace = $db->_aceobj(); Function: Get/Set on the acedb object Returns : Ace object Args : New value of the ace object