Bio::DB GenPept
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Summary
Bio::DB::GenPept - Database object interface to GenPept
Package variables
No package variables defined.
Inherit
Bio::DB::NCBIHelper
Synopsis
    $gb = Bio::DB::GenPept->new();
$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';
    $DEFAULTFORMAT = 'gp';	    
    %PARAMSTRING = ( 
		     'batch' => { 'db'     => 'protein',
				  'usehistory' => 'n',
				  'tool'   => 'bioperl'},
			 # no query?
'gi' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'version' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'single' => { 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, 'webenv' => { 'query_key' => 'querykey', 'WebEnv' => 'cookie', 'db' => 'protein', 'usehistory' => 'n', 'tool' => 'bioperl', 'retmode' => 'text'}, );
}
newdescriptionprevnextTop
sub new {
  my($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;
}

# from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
}
request_formatdescriptionprevnextTop
sub request_format {
    my ($self) = @_;
    return $self->SUPER::request_format($self->default_format());
}

1;
__END__
}
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/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 - 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()