03-25-2013
Both of these work, thank you.
The problem with my original code was obscured by my choice of an example file with unrealistically short sequences. In reality my sequences are longer, and the problem with my code is that it captures headers along with short sequences.
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LEARN ABOUT DEBIAN
go::metadata::panther
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 qw/@species/;
for my $species (@species) {
# do something
}
Or
use GO::Metadata::Panther;
my $s = GO::Metadata::Panther->code('YEAST');
DESCRIPTION
Accesses information related to species in the Panther seq2pthr.gz file. This file can be fetched from:
<ftp://ftp.pantherdb.org/genome/pthr7.0/>
Each item in the exportable @species array contains a hash reference for each species. The items in that hash are:
code
A scalar or the UniProt species code.
ncbi_taxa_id
A scalar reference of NCBI taxa ids that items in the GO database match. This should only be one id, but sometimes it's useful to scan
multiple.
For a complete list of every UniProt species matched to a NCBI taxa <http://www.uniprot.org/docs/speclist>
Constructors
The constructors scans @species for the requested data and returns the object that matches the data. Otherwise it returns a false false.
my $s = GO::Metadata::Panther->code(unicode_species_code)
Return an object filled with the species reference from the UniProtKB species code.
my $s = GO::Metadata::Panther->ncbi(ncbi_taxa_id)
Greate an object from the ncbi_taxa_id.
Function
Functions that can be used outside of the OO interface.
GO::Metadata::Panther::codes()
Returns a list of all UniProt species codes in @species.
GO::Metadata::Panther::valid_codes(unicode_species_code)
Send it a list of panther Unicode codes, returns true if they are all present in @species. Othewise returns false.
OO Function
$s->ncbi_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.
AUTHOR
Sven Heinicke <sven@genomics.princeton.edu</gt>
perl v5.14.2 2010-07-08 GO::Metadata::Panther(3pm)