Bio::DB::GenBank(3)

NAME
Bio::DB::GenBank - Database object interface to GenBank

SYNOPSIS
    $gb = new Bio::DB::GenBank;
    $seq = $gb->get_Seq_by_id('MUSIGHBA1'); # Unique ID
    # or ...
    $seq = $gb->get_Seq_by_acc('J00522'); # Accession Number
    # 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->
    }

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. Batch Entrez support will likely be supported in a future version of DB::GenBank.

Note that when querying for GenBank accessions starting with 'NT_' you will need to call $gb->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).

FEEDBACK

  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

  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://bio.perl.org/bioperl-bugs/

AUTHOR - Aaron Mackey, Jason Stajich
Email amackey@virginia.edu Email jason@chg.mc.duke.edu

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  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

Routines Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI

  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

  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

Routines implemented by Bio::DB::NCBIHelper

  get_request
 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_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.  For large numbers of sequences, this is far superior
            than get_Stream_by_[id/acc]().
  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.

  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

  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()
1; __END__