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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" Bio::DB::CUTG \- for access to the Codon usage Database at http://www.kazusa.or.jp/codon. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 2 \& use Bio::CodonUsage::Table; \& use Bio::DB::CUTG; \& \& my $db = Bio::DB::CUTG\->new(\-sp =>\*(AqPan troglodytes\*(Aq); \& my $CUT = $db\->get_request(); .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" This class retrieves and objectifies codon usage tables either from the \&\s-1CUTG\s0 web database . The idea is that you can initially retrieve a \s-1CUT\s0 from the web database, and write it to file in a way that can be read in later, using the Bio::CodonUsage::IO module. .PP For a web query, two parameters need to be specified: species(sp) and genetic code id (gc). The database is searched using regular expressions, therefore the full latin name must be given to specify the organism. If the species name is ambiguous the first \s-1CUT\s0 in the list is retrieved. Defaults are Homo sapiens and 1(standard genetic code). If you are retrieving CUTs from organisms using other genetic codes this needs to be put in as a parameter. Parameters can be entered in the constructor or in the get_web_request ()method. Allowable parameters are listed in the \f(CW$QUERY_KEYS\fR hash reference variable. .PP I intend at a later date to allow retrieval of multiple codon tables e.g., from a wildcard search. .PP Examples URLs: .PP .SH "SEE ALSO" .IX Header "SEE ALSO" Bio::Tools::CodonTable, Bio::WebAgent, Bio::CodonUsage::Table, Bio::CodonUsage::IO .SH "FEEDBACK" .IX Header "FEEDBACK" .SS "Mailing Lists" .IX Subsection "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. .PP .Vb 2 \& bioperl\-l@bioperl.org \- General discussion \& http://bioperl.org/wiki/Mailing_lists \- About the mailing lists .Ve .SS "Support" .IX Subsection "Support" Please direct usage questions or support issues to the mailing list: .PP \&\fIbioperl\-l@bioperl.org\fR .PP 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. .SS "Reporting Bugs" .IX Subsection "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: .PP .Vb 1 \& https://github.com/bioperl/bioperl\-live/issues .Ve .SH "AUTHORS" .IX Header "AUTHORS" Richard Adams, Richard.Adams@ed.ac.uk .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .SS "new" .IX Subsection "new" .Vb 4 \& 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 .Ve .SS "query_keys" .IX Subsection "query_keys" .Vb 5 \& 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 .Ve .SS "sp" .IX Subsection "sp" .Vb 5 \& 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 .Ve .SS "gc" .IX Subsection "gc" .Vb 5 \& 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 .Ve .SS "get_request" .IX Subsection "get_request" .Vb 5 \& 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) .Ve