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Bio::DB::CUTG(3)      User Contributed Perl Documentation     Bio::DB::CUTG(3)

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:

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

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)

perl v5.14.1			  2011-07-22		      Bio::DB::CUTG(3)
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