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.\" ========================================================================
.\"
.IX Title "GO::Metadata::Panther 3pm"
.TH GO::Metadata::Panther 3pm "2010-07-08" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
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.SH "NAME"
GO::Metadata::Panther \- Species info for data used by Panther Clusters
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\& use GO::Metadata::Panther qw/@species/;
\&
\& for my $species (@species) {
\& # do something
\& }
.Ve
.PP
Or
.PP
.Vb 2
\& use GO::Metadata::Panther;
\& my $s = GO::Metadata::Panther\->code(\*(AqYEAST\*(Aq);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Accesses information related to species in the Panther \fIseq2pthr.gz\fR
file. This file can be fetched from:
.PP
Each item in the exportable \f(CW@species\fR array contains a hash
reference for each species. The items in that hash are:
.IP "code" 4
.IX Item "code"
A scalar or the UniProt species code.
.IP "ncbi_taxa_id" 4
.IX Item "ncbi_taxa_id"
A scalar reference of \s-1NCBI\s0 taxa ids that items in the \s-1GO\s0 database
match. This should only be one id, but sometimes it's useful to scan
multiple.
.PP
For a complete list of every UniProt species matched to a \s-1NCBI\s0 taxa
.SS "Constructors"
.IX Subsection "Constructors"
The constructors scans \f(CW@species\fR for the requested data and returns
the object that matches the data. Otherwise it returns a false false.
.ie n .IP "my $s = GO::Metadata::Panther\->code(\fIunicode_species_code\fR)" 4
.el .IP "my \f(CW$s\fR = GO::Metadata::Panther\->code(\fIunicode_species_code\fR)" 4
.IX Item "my $s = GO::Metadata::Panther->code(unicode_species_code)"
Return an object filled with the species reference from the UniProtKB
species code.
.ie n .IP "my $s = GO::Metadata::Panther\->ncbi(\fIncbi_taxa_id\fR)" 4
.el .IP "my \f(CW$s\fR = GO::Metadata::Panther\->ncbi(\fIncbi_taxa_id\fR)" 4
.IX Item "my $s = GO::Metadata::Panther->ncbi(ncbi_taxa_id)"
Greate an object from the \fIncbi_taxa_id\fR.
.SS "Function"
.IX Subsection "Function"
Functions that can be used outside of the \s-1OO\s0 interface.
.IP "\fIGO::Metadata::Panther::codes()\fR" 4
.IX Item "GO::Metadata::Panther::codes()"
Returns a list of all UniProt species codes in \f(CW@species\fR.
.IP "GO::Metadata::Panther::valid_codes(\fIunicode_species_code\fR)" 4
.IX Item "GO::Metadata::Panther::valid_codes(unicode_species_code)"
Send it a list of panther Unicode codes, returns true if they are all
present in \f(CW@species\fR. Othewise returns false.
.SS "\s-1OO\s0 Function"
.IX Subsection "OO Function"
.ie n .IP "$s\->\fIncbi_ids()\fR" 4
.el .IP "\f(CW$s\fR\->\fIncbi_ids()\fR" 4
.IX Item "$s->ncbi_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.
.SS "\s-1AUTHOR\s0"
.IX Subsection "AUTHOR"
Sven Heinicke