# $Id: GenBank.pm 16139 2009-09-18 21:11:23Z cjfields $
#
# BioPerl module for Bio::DB::GenBank
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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 = Bio::DB::GenBank->new();

    $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 = Bio::DB::GenBank->new(-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

    # don't want the entire sequence or more options
    my $gb = Bio::DB::GenBank->new(-format     => 'Fasta',
                                   -seq_start  => 100,
                                   -seq_stop   => 200,
                                   -strand     => 1,
                                   -complexity => 4);
    my $seqi = $gb->get_Stream_by_query($query);


=head1 DESCRIPTION

Allows the dynamic retrieval of L<Bio::Seq> sequence objects from the
GenBank database at NCBI, via an Entrez query.

WARNING: Please do B<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). The
former behavior prior to bioperl 1.6 was to retrieve these from EBI,
but now these are retrieved directly from NCBI. The older behavior can
be regained by setting the 'redirect_refseq' flag to a value
evaluating to TRUE.

=head2 Running

Alternate methods are described at
L<http://www.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html>

NOTE: strand should be 1 for plus or 2 for minus.

Complexity: gi is often a part of a biological blob, containing other
gis

complexity regulates the display:
  0 - get the whole blob
  1 - get the bioseq for gi of interest (default in Entrez)
  2 - get the minimal bioseq-set containing the gi of interest
  3 - get the minimal nuc-prot containing the gi of interest
  4 - get the minimal pub-set containing the gi of interest

'seq_start' and 'seq_stop' will not work when setting complexity to
any value other than 1.  'strand' works for any setting other than a
complexity of 0 (whole glob); when you try this with a GenBank return
format nothing happens, whereas using FASTA works but causes display
problems with the other sequences in the glob.  As Tao Tao says from
NCBI, "Better left it out or set it to 1."

=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/wiki/Mailing_lists  - About the mailing lists

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=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 the
web:

  http://bugzilla.open-bio.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(%PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE);

use base qw(Bio::DB::NCBIHelper);
BEGIN {    
    $DEFAULTMODE   = 'single';
    $DEFAULTFORMAT = 'gbwithparts';
    %PARAMSTRING = (
			 'batch' => { 'db'     => 'nucleotide',
				  'usehistory' => 'n',
				  'tool'   => 'bioperl'},
		     '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'},
			 'webenv' => {    
				  'query_key'  => 'querykey',
				  'WebEnv'  => 'cookie',
				  '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().
            Caveat: this normally works, but in rare cases simply passing the
            accession can lead to odd results, possibly due to unsynchronized
            NCBI ID servers. Using get_Seq_by_version() is slightly better, but
            using the unique identifier (GI) and get_Seq_by_id is the most
            consistent
  Throws  : "id does not exist" exception

=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)
 Note    : Caveat: this normally works, but using the unique identifier (GI) and
           get_Seq_by_id is the most consistent
 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)

=cut

=head2 default_format

 Title   : default_format
 Usage   : my $format = $self->default_format
 Function: Returns default sequence format for this module
 Returns : string
 Args    : none

=cut

sub default_format {
    return $DEFAULTFORMAT;
}

1;
__END__
