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.\" ========================================================================
.\"
.IX Title "Bio::DB::Ace 3pm"
.TH Bio::DB::Ace 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::DB::Ace \- Database object interface to ACeDB servers
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    $db = Bio::DB::Ace\->new( \-server => \*(Aqmyace.server.com\*(Aq, port => \*(Aq120000\*(Aq);
\&
\&    $seq = $db\->get_Seq_by_id(\*(AqJ00522\*(Aq); # Unique ID
\&
\&    # or ...
\&
\&    $seq = $db\->get_Seq_by_acc(\*(AqJ00522\*(Aq); # Accession Number
.Ve
.SH "DESCRIPTION"
.IX Header "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
.PP
.Vb 1
\&  http://stein.cshl.org/AcePerl/
.Ve
.PP
before this interface will work.
.PP
This interface is designed at the moment to work through a aceclient/aceserver
type mechanism
.SH "INSTALLING ACEPERL"
.IX Header "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
.PP
.Vb 4
\&  Perl Makefile.PL
\&  make
\&  <become root>
\&  make install
.Ve
.PP
Then you will have installed Aceperl. Use the \s-1PREFIX\s0 mechanism to install elsewhere.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Ewan Birney"
.IX Header "AUTHOR - Ewan Birney"
Email birney@ebi.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
.SS "get_Seq_by_id"
.IX Subsection "get_Seq_by_id"
.Vb 5
\& 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
.Ve
.SS "get_Seq_by_acc"
.IX Subsection "get_Seq_by_acc"
.Vb 5
\&  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
.Ve
.SS "_aceobj"
.IX Subsection "_aceobj"
.Vb 5
\&  Title   : _aceobj
\&  Usage   : $ace = $db\->_aceobj();
\&  Function: Get/Set on the acedb object
\&  Returns : Ace object
\&  Args    : New value of the ace object
.Ve