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>