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
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
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)