Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::DB::CUTG.3pm

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)