Bio::DB::Ace(3) User Contributed Perl Documentation Bio::DB::Ace(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::DB::Ace(3)
