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Bio::DB::Ace.3pm

NAME

Bio::DB::Ace - Database object interface to ACeDB servers

SYNOPSIS

     $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
 
     $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
 
     # or ...
 
     $seq = $db->get_Seq_by_acc('J00522'); # Accession Number
 
 

DESCRIPTION

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

   http://stein.cshl.org/AcePerl/
 
 

before this interface will work.

This interface is designed at the moment to work through a aceclient/aceserver type mechanism

INSTALLING ACEPERL

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.

FEEDBACK

Mailing Lists

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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

Reporting Bugs

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Ewan Birney

Email birney@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_Seq_by_id

  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
 
 

get_Seq_by_acc

   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
 
 

_aceobj

   Title   : _aceobj
   Usage   : $ace = $db->_aceobj();
   Function: Get/Set on the acedb object
   Returns : Ace object
   Args    : New value of the ace object