Raw content of Bio::DB::GenBank
<![CDATA[# $Id: GenBank.pm,v 1.47.2.2 2003/07/03 12:31:31 heikki Exp $
#
# BioPerl module for Bio::DB::GenBank
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
# Copyright Aaron Mackey
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
# Added LWP support - Jason Stajich 2000-11-6
# completely reworked by Jason Stajich 2000-12-8
# to use WebDBSeqI
# Added batch entrez back when determined that new entrez cgi will
# essentially work (there is a limit to the number of characters in a
# GET request so I am not sure how we can get around this). The NCBI
# Batch Entrez form has changed some and it does not support retrieval
# of text only data. Still should investigate POST-ing (tried and
# failed) a message to the entrez cgi to get around the GET
# limitations.
=head1 NAME
Bio::DB::GenBank - Database object interface to GenBank
=head1 SYNOPSIS
use Bio::DB::GenBank;
$gb = new Bio::DB::GenBank;
$seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID
# or ...
$seq = $gb->get_Seq_by_acc('J00522'); # Accession Number
$seq = $gb->get_Seq_by_version('J00522.1'); # Accession.version
$seq = $gb->get_Seq_by_gi('405830'); # GI Number
# get a stream via a query string
my $query = Bio::DB::Query::GenBank->new
(-query =>'Oryza sativa[Organism] AND EST',
-reldate => '30',
-db => 'nucleotide');
my $seqio = $gb->get_Stream_by_query($query);
while( my $seq = $seqio->next_seq ) {
print "seq length is ", $seq->length,"\n";
}
# or ... best when downloading very large files, prevents
# keeping all of the file in memory
# also don't want features, just sequence so let's save bandwith
# and request Fasta sequence
$gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' ,
-format => 'Fasta');
my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953'] );
while( my $clone = $seqio->next_seq ) {
print "cloneid is ", $clone->display_id, " ",
$clone->accession_number, "\n";
}
# note that get_Stream_by_version is not implemented
=head1 DESCRIPTION
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the
GenBank 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.
Note that when querying for GenBank accessions starting with 'NT_' you
will need to call $gb-E<gt>request_format('fasta') beforehand, because
in GenBank format (the default) the sequence part will be left out
(the reason is that NT contigs are rather annotation with references
to clones).
Some work has been done to automatically detect and retrieve whole NT_
clones when the data is in that format (NCBI RefSeq clones). More
testing and feedback from users is needed to achieve a good fit of
functionality and ease of use.
=head1 FEEDBACK
=head2 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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 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 email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Aaron Mackey, Jason Stajich
Email amackey@virginia.edu
Email jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the
object methods. Internal methods are usually
preceded with a _
=cut
# Let the code begin...
package Bio::DB::GenBank;
use strict;
use vars qw(@ISA %PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE);
use Bio::DB::NCBIHelper;
@ISA = qw(Bio::DB::NCBIHelper);
BEGIN {
$DEFAULTMODE = 'single';
$DEFAULTFORMAT = 'gp';
%PARAMSTRING = (
'batch' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
'query' => { 'usehistory' => 'y',
'tool' => 'bioperl',
'retmode' => 'text'},
'gi' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
'version' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
'single' => { 'db' => 'nucleotide',
'usehistory' => 'n',
'tool' => 'bioperl',
'retmode' => 'text'},
);
}
# new is in NCBIHelper
# helper method to get db specific options
=head2 new
Title : new
Usage : $gb = Bio::DB::GenBank->new(@options)
Function: Creates a new genbank handle
Returns : New genbank handle
Args : -delay number of seconds to delay between fetches (3s)
NOTE: There are other options that are used internally. By NCBI policy, this
module introduces a 3s delay between fetches. If you are fetching multiple genbank
ids, it is a good idea to use get
=cut
=head2 get_params
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
=cut
sub get_params {
my ($self, $mode) = @_;
return defined $PARAMSTRING{$mode} ?
%{$PARAMSTRING{$mode}} : %{$PARAMSTRING{$DEFAULTMODE}};
}
# from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
=head1 Routines Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
=head2 get_Seq_by_id
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
=head2 get_Seq_by_acc
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc($acc);
Function: Gets a Seq object by accession numbers
Returns : a Bio::Seq object
Args : the accession number as a string
Note : For GenBank, this just calls the same code for get_Seq_by_id()
Throws : "id does not exist" exception
=cut
sub get_Seq_by_acc {
my ($self,$seqid) = @_;
$self->SUPER::get_Seq_by_acc("gb|$seqid");
}
=head2 get_Seq_by_gi
Title : get_Seq_by_gi
Usage : $seq = $db->get_Seq_by_gi('405830');
Function: Gets a Bio::Seq object by gi number
Returns : A Bio::Seq object
Args : gi number (as a string)
Throws : "gi does not exist" exception
=head2 get_Seq_by_version
Title : get_Seq_by_version
Usage : $seq = $db->get_Seq_by_version('X77802.1');
Function: Gets a Bio::Seq object by sequence version
Returns : A Bio::Seq object
Args : accession.version (as a string)
Throws : "acc.version does not exist" exception
=head1 Routines implemented by Bio::DB::NCBIHelper
=head2 get_Stream_by_query
Title : get_Stream_by_query
Usage : $seq = $db->get_Stream_by_query($query);
Function: Retrieves Seq objects from Entrez 'en masse', rather than one
at a time. For large numbers of sequences, this is far superior
than get_Stream_by_[id/acc]().
Example :
Returns : a Bio::SeqIO stream object
Args : $query : An Entrez query string or a
Bio::DB::Query::GenBank object. It is suggested that you
create a Bio::DB::Query::GenBank object and get the entry
count before you fetch a potentially large stream.
=cut
=head2 get_Stream_by_id
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
=head2 get_Stream_by_acc
Title : get_Stream_by_acc
Usage : $seq = $db->get_Stream_by_acc([$acc1, $acc2]);
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()
=cut
=head2 get_Stream_by_gi
Title : get_Stream_by_gi
Usage : $seq = $db->get_Seq_by_gi([$gi1, $gi2]);
Function: Gets a series of Seq objects by gi numbers
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of gi numbers for
the desired sequence entries
Note : For GenBank, this just calls the same code for get_Stream_by_id()
=head2 get_Stream_by_batch
Title : get_Stream_by_batch
Usage : $seq = $db->get_Stream_by_batch($ref);
Function: Retrieves Seq objects from Entrez 'en masse', rather than one
at a time.
Example :
Returns : a Bio::SeqIO stream object
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
NOTE: This method is redundant and deprecated. Use get_Stream_by_id()
instead.
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
1;
__END__
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