Chris Mungall > go-perl-0.14 > GO::Metadata::Panther

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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

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>

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