Bio::DB::XEMBL - Database object interface for XEMBL entry retrieval 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"; } Allows the dynamic retrieval of Bio::Seq objects from the XEMBL database. See Bio::Seq for details.

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://bio.perl.org/MailList.html - 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://bugzilla.bioperl.org/ Email Lincoln Stein <lstein@cshl.org> 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.