Bio::DB GenPept
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::DB::GenPept - Database object interface to GenPept
Package variables
No package variables defined.
Included modules
Bio::DB::NCBIHelper
Inherit
Bio::DB::NCBIHelper
Synopsis
    $gb = new Bio::DB::GenPept;

    $seq = $gb->get_Seq_by_id('195055'); # Unique ID

    # or ...

    $seq = $gb->get_Seq_by_acc('DEECTH'); # Accession Number

    my $seqio = $gb->get_Stream_by_id(['195055', 'DEECTH']);
    while( my $seq = $seqio->next_seq ) {
	print "seq is is ", $seq->display_id, "\n";
    }
Description
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept
database at NCBI, via an Entrez query.
WARNING: Please do NOT spam the Entrez web server with multiple requests.
NCBI offers Batch Entrez for this purpose. Batch Entrez support will likely
be supported in a future version of DB::GenPept.
Currently the only return format supported by NCBI Entrez for GenPept
database is GenPept format, so any format specification passed to
GenPept will be ignored still be forced to GenPept format (which is
just GenBank format).
Methods
BEGIN Code
new
No description
Code
get_paramsDescriptionCode
default_formatDescriptionCode
request_formatDescriptionCode
Methods description
get_paramscode    nextTop
 Title   : get_params
 Usage   : my %params = $self->get_params($mode)
 Function: Returns key,value pairs to be passed to NCBI database
           for either 'batch' or 'single' sequence retrieval method
 Returns : a key,value pair hash
 Args    : 'single' or 'batch' mode for retrieval
default_formatcodeprevnextTop
 Title   : default_format
 Usage   : my $format = $self->default_format
 Function: Returns default sequence format for this module
 Returns : string
 Args    : none
request_formatcodeprevnextTop
 Title   : request_format
 Usage   : my $format = $self->request_format;
           $self->request_format($format);
 Function: Get/Set sequence format retrieval
 Returns : string representing format
 Args    : $format = sequence format
Methods code
BEGINTop
BEGIN {
     $DEFAULTMODE   = 'single';
    $DEFAULTFORMAT = 'gp';	    
    %PARAMSTRING = ( 
		     'batch' => { 'db'     => 'protein',
				  'usehistory' => 'n',
				  'tool'   => 'bioperl',
				  'retmode' => 'text'},
		     'gi' => { 'db'     => 'protein',
			       'usehistory' => 'n',
			       'tool'   => 'bioperl',
			       'retmode' => 'text'},
		     'version' => { 'db'     => 'protein',
				    'usehistory' => 'n',
				    'tool'   => 'bioperl',
				    'retmode' => 'text'},
		     'single' => { 'db'     => 'protein',
				   'usehistory' => 'n',
				   'tool'   => 'bioperl',
				   'retmode' => 'text'},
		     );
}
newdescriptionprevnextTop
sub new {
  my($class, @args) = @_;
  my $self = $class->SUPER::new(@args);
  $self->request_format($self->default_format);
  return $self;
}
get_paramsdescriptionprevnextTop
sub get_params {
    my ($self, $mode) = @_;
    return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}};
}
default_formatdescriptionprevnextTop
sub default_format {
    return $DEFAULTFORMAT;
}
request_formatdescriptionprevnextTop
sub request_format {
    my ($self) = @_;
    return $self->SUPER::request_format($self->default_format());
}
General documentation
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/MailList.shtml  - About the mailing lists
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 email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Aaron Mackey, Jason StajichTop
Email amackey@virginia.edu
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessITop
get_Seq_by_idTop
 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
 Function: Gets a Bio::Seq object by its name
 Returns : a Bio::Seq object
 Args    : the id (as a string) of a sequence
 Throws  : "id does not exist" exception
get_Seq_by_accTop
  Title   : get_Seq_by_acc
  Usage   : $seq = $db->get_Seq_by_acc('AAC73346');
  Function: Gets a Seq objects by accession number
  Returns : Bio::Seq object
  Args    : accession number to retrive by
Routines implemented by Bio::DB::NCBIHelperTop
get_requestTop
 Title   : get_request
 Usage   : my $url = $self->get_request
 Function: HTTP::Request
 Returns : 
 Args    : %qualifiers = a hash of qualifiers (ids, format, etc)
get_Stream_by_idTop
  Title   : get_Stream_by_id
  Usage   : $stream = $db->get_Stream_by_id( [$uid1, $uid2] );
  Function: Gets a series of Seq objects by unique identifiers
  Returns : a Bio::SeqIO stream object
  Args    : $ref : a reference to an array of unique identifiers for
                   the desired sequence entries
get_Stream_by_acc (2)Top
  Title   : get_Stream_by_acc
  Usage   : $seq = $db->get_Stream_by_acc($acc);
  Function: Gets a series of Seq objects by accession numbers
  Returns : a Bio::SeqIO stream object
  Args    : $ref : a reference to an array of accession numbers for
                   the desired sequence entries
  Note    : For GenBank, this just calls the same code for get_Stream_by_id()