Bio::DB::XEMBL.3pm

Langue: en

Autres versions - même langue

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   use Bio::DB::XEMBL;
 
   $embl = new Bio::DB::XEMBL;
 
   # remember that XEMBL_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 ...
   $seq = $embl->get_Seq_by_acc('J02231'); # XEMBL 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'); # XEMBL VERSION
   };
   print "cloneid is ", $seq->id, "\n" unless $@;
 
   my $seqio = $embl->get_Stream_by_batch(['U83300','U83301','U83302']);
   while( my $clone =  $seqio->next_seq ) {
         print "cloneid is ", $clone->id, "\n";
   }
 
 

DESCRIPTION

Allows the dynamic retrieval of Bio::Seq objects from the XEMBL database. See Bio::Seq for details.

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
 
 

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 - Lincoln Stein

Email Lincoln Stein <lstein@cshl.org>

APPENDIX

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

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_Stream_by_batch

   Title   : get_Stream_by_batch
   Usage   : $seq = $db->get_Stream_by_batch($ref);
   Function: Retrieves Seq objects from XEMBL 'en masse', rather than one
             at a time. Currently this is not particularly efficient, as
             it loads the entire result into memory and parses it.
   Example :
   Returns : a Bio::SeqIO stream object
   Args    : $ref : an array reference containing a list of unique 
             ids/accession numbers.
 
 

get_Seq_by_acc

  Title   : get_Seq_by_acc
  Usage   : $seq = $db->get_Seq_by_acc('X77802');
  Function: Gets a Bio::Seq object by accession number
  Returns : A Bio::Seq object
  Args    : accession number (as a string)
  Throws  : "acc 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
 
 

endpoint

  Title   : endpoint
  Usage   : $endpoint = $db->endpoint([$endpoint])
  Function: Gets/sets endpoint for SOAP connection
  Returns : old endpoint
  Args    : new endpoint(optional)
 
 

new_from_registry

  Title   : new_from_registry
  Usage   : $db = Bio::DB::XEMBL->new_from_registry(%config)
  Function: creates a new Bio::DB::XEMBL object in a Bio::DB::Registry-
            compatible fashion
  Returns : new Bio::DB::XEMBL
  Args    : provided by the registry, see below
  Status  : Public
 
 

The following registry-configuration tags are recognized:

   location     Endpoint for the XEMBL service.  Currently the only
                known valid endpoint is 
                http://www.ebi.ac.uk:80/cgi-bin/xembl/XEMBL-SOAP.pl
 
 

NOTE: Since this info is supposed to be coming from WSDL, the location is currently ignored.