Bio::DB::CUTG(3) for access to the Codon usage Database

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.

Examples URLs:

<http://www.kazusa.or.jp/codon/cgi-bin/spsearch.cgi?species=Pan+troglodytes&c=s> <http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=37011&aa=1&style=GCG>

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. 

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

AUTHORS

Richard Adams, [email protected]

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)

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