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.
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Email Lincoln Stein <lstein@cshl.org>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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.
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
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
Title : endpoint Usage : $endpoint = $db->endpoint([$endpoint]) Function: Gets/sets endpoint for SOAP connection Returns : old endpoint Args : new endpoint(optional)
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.