Ewan Birney

NAME

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

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

    # 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

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->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.

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@bioperl.org

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

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

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

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()

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()

1; __END__