Bio::DB
GenPept
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Summary
Bio::DB::GenPept - Database object interface to GenPept
Package variables
No package variables defined.
Included modules
Inherit
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
Methods description
Title : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Returns : string
Args : none |
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 |
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
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'},
);} | sub default_format
{ return $DEFAULTFORMAT;
}
} | sub get_params
{ my ($self, $mode) = @_;
return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}};} | sub new
{ my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->request_format($self->default_format);
return $self; } | sub request_format
{ my ($self) = @_;
return $self->SUPER::request_format($self->default_format());
}
1;
__END__} | General documentation
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| AUTHOR - Aaron Mackey, Jason Stajich | Top |
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::RandomAccessI | Top |
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
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::NCBIHelper | Top |
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
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
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()