/ 
go-perl-0.13
River stage one • 1 direct dependent • 1 total dependent
/ GO::Metadata::Panther

NAME

GO::Metadata::Panther - Species info for data used by Panther Clusters

SYNOPSIS

use GO::Metadata::Panther qw/@species/;

for my $species (@species) {
 # do something
}

Or

use GO::Metadata::Panther;
my $s = GO::Metadata::Panther->code('YEAST');

DESCRIPTION

Accesses information related to species in the Panther seq2pthr.gz file. This file can be fetched from: ftp://ftp.pantherdb.org/genome/pthr7.0/

Each item in the exportable @species array contains a hash reference for each species. The items in that hash are:

code

A scalar or the UniProt species code.

ncbi_taxa_id

A scalar reference of NCBI taxa ids that items in the GO database match. This should only be one id, but sometimes it's useful to scan multiple.

For a complete list of every UniProt species matched to a NCBI taxa http://www.uniprot.org/docs/speclist

Constructors

The constructors scans @species for the requested data and returns the object that matches the data. Otherwise it returns a false false.

my $s = GO::Metadata::Panther->code(unicode_species_code)

Return an object filled with the species reference from the UniProtKB species code.

my $s = GO::Metadata::Panther->ncbi(ncbi_taxa_id)

Greate an object from the ncbi_taxa_id.

Function

Functions that can be used outside of the OO interface.

GO::Metadata::Panther::codes()

Returns a list of all UniProt species codes in @species.

GO::Metadata::Panther::valid_codes(unicode_species_code)

Send it a list of panther Unicode codes, returns true if they are all present in @species. Othewise returns false.

OO Function

$s->ncbi_ids()

Returns the list of NCBI taxa identifiers associated with the UniProt species code. In a perfect word this will only every return one value. In any case, the first value will be the actual numeric identifier associated.

AUTHOR

Sven Heinicke <sven@genomics.princeton.edu</gt>