/ 
bioperl-1.5.2_004-RCb
/ Bio::DB::XEMBL

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.