Bio::DB::Ace - Database object interface to ACeDB servers
Contents
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
perl v5.30.0 2019-11-25 Bio::DB::Ace(3pm)
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
Feedback
MailingLists
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.
ReportingBugs
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
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.
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
