NAME

Bio::DB::DBFetch - Database object for retrieving using the dbfetch script

SYNOPSIS

#do not use this module directly

DESCRIPTION

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.

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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho

Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>

APPENDIX

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

Routines from Bio::DB::WebDBSeqI

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

Bio::DB::DBFetch specific routines

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

Bio::DB::DBFetch routines

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq