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Summary

Bio::DB::EMBL - Database object interface for EMBL entry retrieval

Package variables

Included modules

Inherit

Bio::DB::DBFetch

Synopsis

  use Bio::DB::EMBL;

  $embl = Bio::DB::EMBL->new();

  # remember that EMBL_ID does not equal GenBank_ID!
  $seq = $embl->get_Seq_by_id('BUM'); # EMBL ID
  print "cloneid is ", $seq->id, "\n";

  # or changeing to accession number and Fasta format ...
  $embl->request_format('fasta');
  $seq = $embl->get_Seq_by_acc('J02231'); # EMBL ACC
  print "cloneid is ", $seq->id, "\n";

  # especially when using versions, you better be prepared
  # in not getting what what want
  eval {
      $seq = $embl->get_Seq_by_version('J02231.1'); # EMBL VERSION
  };
  print "cloneid is ", $seq->id, "\n" unless $@;

  # 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
  $embl = Bio::DB::EMBL->new(-retrievaltype => 'tempfile' ,
 			    -format => 'fasta');
  my $seqio = $embl->get_Stream_by_id(['AC013798', 'AC021953'] );
  while( my $clone =  $seqio->next_seq ) {
 	print "cloneid is ", $clone->id, "\n";
  }

Description

Allows the dynamic retrieval of sequence objects Bio::Seq from the
EMBL database using the dbfetch script at EBI:
http://www.ebi.ac.uk/Tools/dbfetch/dbfetch.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
The functionality of this module is inherited from Bio::DB::DBFetch
which implements Bio::DB::WebDBSeqI.

Methods

Methods description

 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)

  Title   : get_Stream_by_acc
  Usage   : $seq = $db->get_Seq_by_acc([$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()

  Title   : _check_id
  Usage   : 
  Function: 
  Returns : A Bio::DB::RefSeq reference or throws
  Args    : $id(s), $string

Methods code

BEGIN {

    # you can add your own here theoretically.
    %HOSTS = (
	       'dbfetch' => {
		   baseurl => 'http://%s/Tools/dbfetch/dbfetch?db=embl&style=raw',
		   hosts   => {
		       'ebi'  => 'www.ebi.ac.uk'
		       }
	       }
	      );
    %FORMATMAP = ( 'embl' => 'embl',
		   'fasta' => 'fasta'
		   );
    $DEFAULTFORMAT = 'embl';

}

sub new {

    my ($class, @args ) = @_;
    my $self = $class->SUPER::new(@args);

    $self->{ '_hosts' } = {};
    $self->{ '_formatmap' } = {};

    $self->hosts(\%HOSTS);
    $self->formatmap(\%FORMATMAP);
    $self->{'_default_format'} = $DEFAULTFORMAT;

    return $self;

}

sub get_Stream_by_acc {

    my ($self, $ids ) = @_;
    my $newdb = $self->_check_id($ids);
    if ($newdb && $newdb->isa('Bio::DB::RefSeq')) {
	return $newdb->get_seq_stream('-uids' => $ids, '-mode' => 'single');
    } else {
	return $self->get_seq_stream('-uids' => $ids, '-mode' => 'single');
    }

}

sub _check_id {

    my ($self, $ids) = @_;

    # NT contigs can not be retrieved
    $self->throw("NT_ contigs are whole chromosome files which are not part of regular".
		 "database distributions. Go to ftp://ftp.ncbi.nih.gov/genomes/.") 
	if $ids =~ /NT_/;

    # Asking for a RefSeq from EMBL/GenBank

    if ($ids =~ /N._/) {
	$self->warn("[$ids] is not a normal sequence entry but a RefSeq entry.".
		   " Redirecting the request.\n")
	    if $self->verbose >= 0;
	return  Bio::DB::RefSeq->new(-verbose => $self->verbose);
    }
}


1;

}

General documentation

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

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

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:

  https://redmine.open-bio.org/projects/bioperl/

Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>

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

Overriding WebDBSeqI method to help newbies to retrieve sequences.
EMBL database is all too often passed RefSeq accessions. This
redirects those calls. See Bio::DB::RefSeq.