Bio::DB::DBFetch - Database object for retrieving using the dbfetch script #do not use this module directly Allows the dynamic retrieval of entries from databases using the dbfetch script at EBI: <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. This is a superclass which is called by instantiable subclasses with correct parameters.

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 Heikki Lehvaslaiho <Heikki@ebi.ac.uk> The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_request
Title : get_request Usage : my $url = $self->get_request Function: returns a HTTP::Request object Returns : Args : %qualifiers = a hash of qualifiers (ids, format, etc)

postprocess_data
Title : postprocess_data Usage : $self->postprocess_data ( 'type' => 'string', 'location' => \$datastr); Function: process downloaded data before loading into a Bio::SeqIO Returns : void Args : hash with two keys - 'type' can be 'string' or 'file' - 'location' either file location or string reference containing data

default_format
Title : default_format Usage : my $format = $self->default_format Function: Returns default sequence format for this module Returns : string Args : none

get_Stream_by_id
Title : get_Stream_by_id Usage : $seq = $db->get_Stream_by_id($ref); Function: Retrieves Seq objects from the server 'en masse', rather than one at a time. For large numbers of sequences, this is far superior than get_Stream_by_[id/acc](). Example : Returns : a Bio::SeqIO stream object Args : $ref : either an array reference, a filename, or a filehandle from which to get the list of unique ids/accession numbers. NOTE: for backward compatibility, this method is also called get_Stream_by_batch.

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 accession number Returns : A Bio::Seq object Args : version number (as a string) Throws : "version does not exist" exception

request_format
Title : request_format Usage : my ($req_format, $ioformat) = $self->request_format; $self->request_format("genbank"); $self->request_format("fasta"); Function: Get/Set sequence format retrieval. The get-form will normally not be used outside of this and derived modules. Returns : Array of two strings, the first representing the format for retrieval, and the second specifying the corresponding SeqIO format. Args : $format = sequence format

servertype
Title : servertype Usage : my $servertype = $self->servertype $self->servertype($servertype); Function: Get/Set server type Returns : string Args : server type string [optional]

hostlocation
Title : hostlocation Usage : my $location = $self->hostlocation() $self->hostlocation($location) Function: Set/Get Hostlocation Returns : string representing hostlocation Args : string specifying hostlocation [optional]

location_url
Title : location Usage : my $url = $self->location_url() Function: Get host url Returns : string representing url Args : none These methods allow subclasses to pass parameters.

hosts
Title : hosts Usage : Function: get/set for host hash Returns : Args : optional hash

formatmap
Title : formatmap Usage : Function: get/set for format hash Returns : Args : optional hash