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Manual Reference Pages  -  BIO::DB::DBFETCH (3)

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NAME

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

CONTENTS

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



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perl v5.20.3 BIO::DB::DBFETCH (3) 2016-04-05

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