Scroll to navigation

GO::Metadata::Panther(3pm) User Contributed Perl Documentation GO::Metadata::Panther(3pm)

NAME

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

SYNOPSIS

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

DESCRIPTION

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/>

Exportable Subroutines

Returns the list of UniProt species codes that are used in Panther clusters.
Returns a list of "GO::Metadata::Panther" objects that are used in Panther clusters.
Returns a true value in every argument is a UniProt species code used in Panther cluster. Otherwise returns false.

OO Function

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>

2023-12-18 perl v5.36.0