Bio::DB::EMBL.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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/cgi-bin/dbfetch <http://www.ebi.ac.uk/cgi-bin/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.

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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.

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/
 
 

AUTHOR - Heikki Lehvaslaiho

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

APPENDIX

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

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.

Bio::DB::WebDBSeqI methods

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.

get_Stream_by_acc

   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()
 
 

_check_id

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