Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::DB::CUTG - for access to the Codon usage Database at http://www.kazusa.or.jp/codon.

SYNOPSIS

              use Bio::CodonUsage::Table;
              use Bio::DB::CUTG;

              my $db = Bio::DB::CUTG->new(-sp =>'Pan troglodytes');
              my $CUT = $db->get_request();

DESCRIPTION

       This class retrieves and objectifies codon usage tables either from the CUTG web database
       . The idea is that you can initially retrieve a CUT from the web database, and write it to
       file in a way that can be read in later, using the Bio::CodonUsage::IO module.

       For a web query, two parameters need to be specified: species(sp) and genetic code id
       (gc). The database is searched using regular expressions, therefore the full latin name
       must be given to specify the organism. If the species name is ambiguous the first CUT in
       the list is retrieved.  Defaults are Homo sapiens and 1(standard genetic code).  If you
       are retrieving CUTs from organisms using other genetic codes this needs to be put in as a
       parameter. Parameters can be entered in the constructor or in the get_web_request
       ()method. Allowable parameters are listed in the $QUERY_KEYS hash reference variable.

       I intend at a later date to allow retrieval of multiple codon tables e.g., from a wildcard
       search.

SEE ALSO

       Bio::Tools::CodonTable, Bio::WebAgent, Bio::CodonUsage::Table, Bio::CodonUsage::IO

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/

AUTHORS

       Richard Adams, Richard.Adams@ed.ac.uk

APPENDIX

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

   new
        Title   : new
        Usage   : my $db = Bio::DB::CUTG->new()
        Returns : a reference to a new Bio::DB::CUTG
        Args    : hash of optional values for db query

   query_keys
        Title   : query_keys
        Usage   : $db->query_keys()
        Purpose : To determine valid keys for parameters for db query.
        Returns : a reference to a hash describing valid query keys
        Args    : none

   sp
        Title  : sp
        Usage  : my $sp = $db->sp();
        Purpose: Get/set method for species name
        Returns: void or species name string
        Args   : None or species name string

   gc
        Title  : gc
        Usage  : my $gc = $db->gc();
        Purpose: Get/set method for genetic code id
        Returns: void or genetic code  integer
        Args   : None or genetic code integer

   get_request
        Title  : get_request
        Usage  : my $cut = $db->get_request();
        Purpose: To query remote CUT with a species name
        Returns: a new codon usage table object
        Args   : species  name(mandatory), genetic code id(optional)