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.\" ========================================================================
.\"
.IX Title "GO::Metadata::Panther 3pm"
.TH GO::Metadata::Panther 3pm "2021-01-09" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
GO::Metadata::Panther \- Species info for data used by Panther Clusters
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& use GO::Metadata::Panther;
\& my $s = GO::Metadata::Panther\->code(\*(AqYEAST\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Inherits functions from GO::Metadata::UniProt::Species.
.PP
Accesses information related to species in the Panther \fIseq2pthr.gz\fR
file.  This file can be fetched from:
<ftp://ftp.pantherdb.org/genome/pthr7.0/>
.SS "Exportable Subroutines"
.IX Subsection "Exportable Subroutines"
.IP "\fBpanther_codes()\fR" 4
.IX Item "panther_codes()"
Returns the list of UniProt species codes that are used in Panther clusters.
.IP "GO::Metadata::Panther\->\fBpanther_all()\fR" 4
.IX Item "GO::Metadata::Panther->panther_all()"
Returns a list of \f(CW\*(C`GO::Metadata::Panther\*(C'\fR objects that are used in Panther clusters.
.IP "valid_codes(...)" 4
.IX Item "valid_codes(...)"
Returns a true value in every argument is a UniProt species code used
in Panther cluster.  Otherwise returns false.
.SS "\s-1OO\s0 Function"
.IX Subsection "OO Function"
.IP "GO::Metadata::Panther\->new(...);" 4
.IX Item "GO::Metadata::Panther->new(...);"
This basically hands things off to GO::Metadata::UniProt::Species's
new function.   Populates that with other Panther/GO specific
information, and does some error correction.
.ie n .IP "$s\->\fBncbi_taxa_ids()\fR" 4
.el .IP "\f(CW$s\fR\->\fBncbi_taxa_ids()\fR" 4
.IX Item "$s->ncbi_taxa_ids()"
Returns the list of \s-1NCBI\s0 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.
.ie n .IP "$s\->\fBprefers()\fR" 4
.el .IP "\f(CW$s\fR\->\fBprefers()\fR" 4
.IX Item "$s->prefers()"
Returns a list of id types (generally to be populated in
\&\f(CW\*(C`dbxref.xref_dbname\*(C'\fR) in order of preference of use.  If a null list,
we have never encountered a conflict that needed resolving.
.SS "\s-1SEE ALSO\s0"
.IX Subsection "SEE ALSO"
GO::Metadata::UniProt::Species
.SS "\s-1AUTHOR\s0"
.IX Subsection "AUTHOR"
Sven Heinicke <sven@genomics.princeton.edu</gt>