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Bio::DB::DBFetch.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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