Bio::DB CUTG
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Summary
Bio::DB::CUTG - for access to the Codon usage Database
at http://www.kazusa.or.jp/codon.
Package variables
Globals (from "use vars" definitions)
$QUERY_KEYS
$URL
Included modules
Bio::CodonUsage::IO
IO::String
URI::Escape
Inherit
Bio::WebAgent
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
Methods
BEGIN Code
newDescriptionCode
query_keysDescriptionCode
spDescriptionCode
gcDescriptionCode
get_requestDescriptionCode
_check_args
No description
Code
_db
No description
Code
Methods description
newcode    nextTop
 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_keyscodeprevnextTop
 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
spcodeprevnextTop
 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
gccodeprevnextTop
 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_requestcodeprevnextTop
 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)
Methods code
BEGINTop
BEGIN {
    $URL = "http://www.kazusa.or.jp";
}
newdescriptionprevnextTop
sub new {
    my ( $class, @args ) = @_;
    _check_args(@args);
    my $self = $class->SUPER::new(@args);
    return $self;
}
query_keysdescriptionprevnextTop
sub query_keys {
    return $QUERY_KEYS;
}
spdescriptionprevnextTop
sub sp {
    my $self = shift;
    if (@_) {
        my $name = shift;
        $self->{'_sp'} = $name;
    }
    return $self->{'_sp'} || "Homo sapiens";
}
gcdescriptionprevnextTop
sub gc {
    #### genetic code id for translations ####
my $self = shift; if (@_) { if ( $_[0] =~ /^\d+$/ && $_[0] >= 1 && $_[0] <= 15 && $_[0] != 7 && $_[0] != 8 ) { $self->{'_gc'} = shift; } else { $self->warn( "invalid genetic code index - setting to standard default (1)"); $self->{'_gc'} = 1; } } return $self->{'_gc'} || 1; #return 1 if not defined
}
get_requestdescriptionprevnextTop
sub get_request {
    my ( $self, @args ) = @_;
    _check_args(@args);
    shift;
    ### can put in parameters here as well
while (@_) { my $key = shift; $key =~ s/^-//; $self->$key(shift); } $self->url($URL); ###1st of all search DB to check species exists and is unique
my $nameparts = join "+", $self->sp =~ /(\S+)/g; my $search_url = $self->url . "/codon/cgi-bin/spsearch.cgi?species=" . $nameparts . "&c=s"; my $rq = HTTP::Request->new( GET => $search_url ); my $reply = $self->request($rq); if ( $reply->is_error ) { $self->throw( $reply->as_string() . "\nError getting for url $search_url!\n" ); } my $content = $reply->content; return 0 unless $content; $self->debug(" reply from query is\n $content"); ##### if no matches, assign defaults - or can throw here? ######
if ( $content =~ /not found/i ) { $self->warn("organism not found -selecting human [9606] as default"); $self->sp("9606"); $self->_db("gbpri"); } else { my @names = $content =~ /species=([^"]+)/g; ### get 1st species data from report ####
my @dbs = $content =~ /\[([^\]]+)\]:\s+\d+/g; ## warn if more than 1 matching species ##
## if multiple species retrieved, choose first one by default ##
$self->throw("No names returned for $nameparts") unless @names; if ( @names > 1 ) { $self->warn( "too many species - not a unique species id\n" . "selecting $names[0] using database [$dbs[0]]" ); } ### now assign species and database value
$self->sp( $names[0] ); $self->_db( $dbs[0] ); } ######## now get codon table , all defaults established now
##construct URL##
$nameparts = $self->sp; my $CT_url = $self->url . "/codon/cgi-bin/showcodon.cgi?species=" . $nameparts . "&aa=" . $self->gc . "&style=GCG"; $self->debug("URL : $CT_url\n"); ## retrieve data in html##
my $rq2 = HTTP::Request->new( GET => $CT_url ); $reply = $self->request($rq2); if ( $reply->is_error ) { $self->throw( $reply->as_string() . "\nError getting for url $CT_url!\n" ); } my $content2 = $reply->content; ## strip html tags, basic but works here
$content2 =~ s/<[^>]+>//sg; $content2 =~ s/Format.*//sg; $self->debug("raw DDB table is :\n $content2"); ### and pass to Bio::CodonUsage::IO for parsing
my $iostr = IO::String->new($content2); my $io = Bio::CodonUsage::IO->new( -fh => $iostr ); ##return object ##
return $io->next_data;
}
_check_argsdescriptionprevnextTop
sub _check_args {
    ###checks parameters for matching $QUERYKEYS
my @args = @_; while ( my $key = shift @args ) { $key = lc($key); $key =~ s/\-//; if ( !exists( $QUERY_KEYS->{$key} ) ) { Bio::Root::Root->throw( "invalid parameter - must be one of [" . ( join "] [", keys %$QUERY_KEYS ) . "]" ); } shift @args; } } #### internal URL parameter not specifiable ######
}
_dbdescriptionprevnextTop
sub _db {
    my $self = shift;
    if (@_) {
        $self->{'_db'} = shift;
    }
    return $self->{'_db'};
}

1;
}
General documentation
SEE ALSOTop
Bio::Tools::CodonTable,
Bio::WebAgent,
Bio::CodonUsage::Table,
Bio::CodonUsage::IO
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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/
AUTHORSTop
Richard Adams, Richard.Adams@ed.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _