GO::Metadata::Panther - Species info for data used by Panther
Clusters
use GO::Metadata::Panther;
my $s = GO::Metadata::Panther->code('YEAST');
Inherits functions from GO::Metadata::UniProt::Species.
Accesses information related to species in the Panther
seq2pthr.gz file. This file can be fetched from:
<ftp://ftp.pantherdb.org/genome/pthr7.0/>
- panther_codes()
- Returns the list of UniProt species codes that are used in Panther
clusters.
- GO::Metadata::Panther->panther_all()
- Returns a list of
"GO::Metadata::Panther" objects that are
used in Panther clusters.
- valid_codes(...)
- Returns a true value in every argument is a UniProt species code used in
Panther cluster. Otherwise returns false.
OO Function
- GO::Metadata::Panther->new(...);
- This basically hands things off to GO::Metadata::UniProt::Species's new
function. Populates that with other Panther/GO specific information, and
does some error correction.
- $s->ncbi_taxa_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.
- $s->prefers()
- Returns a list of id types (generally to be populated in
"dbxref.xref_dbname") in order of
preference of use. If a null list, we have never encountered a conflict
that needed resolving.
SEE ALSO
GO::Metadata::UniProt::Species
AUTHOR
Sven Heinicke <sven@genomics.princeton.edu</gt>