GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::DB::ACE (3)

.ds Aq ’

NAME

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

CONTENTS

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



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::DB::ACE (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.