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('J00522'); # 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:

  https://github.com/bioperl/bioperl-live/issues

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