Bio::DB Ace
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Summary
Bio::DB::Ace - Database object interface to ACeDB servers
Package variables
No package variables defined.
Included modules
Bio::Seq
Inherit
Bio::DB::RandomAccessI
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
Methods
BEGIN Code
new
No description
Code
get_Seq_by_idDescriptionCode
get_Seq_by_accDescriptionCode
_aceobjDescriptionCode
Methods description
get_Seq_by_idcode    nextTop
 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_acccodeprevnextTop
  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
_aceobjcodeprevnextTop
  Title   : _aceobj
Usage : $ace = $db->_aceobj();
Function: Get/Set on the acedb object
Returns : Ace object
Args : New value of the ace object
Methods code
BEGINTop
BEGIN {
  eval "require Ace;";
  if( $@) {
    print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@";
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my ($host,$port) = $self->_rearrange([qw(
					 HOST
					 PORT
					 )],
				     @args,
				     );

  if( !$host || !$port ) {
    $self->throw("Must have a host and port for an acedb server to work");
  }

  my $aceobj = Ace->connect(-host => $host,
			    -port => $port) ||
			      $self->throw("Could not make acedb object to $host:$port");

  $self->_aceobj($aceobj);


  return $self;
}
get_Seq_by_iddescriptionprevnextTop
sub get_Seq_by_id {
  my $self = shift;
  my $id = shift or $self->throw("Must supply an identifier!\n");
  my $ace = $self->_aceobj();
  my ($seq,$dna,$out);

  $seq = $ace->fetch( 'Sequence' , $id);

  # get out the sequence somehow!
$dna = $seq->asDNA(); $dna =~ s/^>.*\n//; $dna =~ s/\n//g; $out = Bio::Seq->new( -id => $id, -alphabet => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id"); return $out;
}
get_Seq_by_accdescriptionprevnextTop
sub get_Seq_by_acc {
  my $self = shift;
  my $acc = shift or $self->throw("Must supply an accession number!\n");

  return $self->get_Seq_by_id($acc);
}
_aceobjdescriptionprevnextTop
sub _aceobj {
  my ($self,$arg) = @_;

  if( $arg ) {
    $self->{'_aceobj'} = $arg;
  }

  return $self->{'_aceobj'};
}

1;
}
General documentation
INSTALLING ACEPERLTop
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.
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _