Provided by: libbio-perl-perl_1.7.2-3_all bug

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://github.com/bioperl/bioperl-live/issues

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