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