[Bioperl-l] Retrieving taxonomy information from a GenBank file
torsten.seemann at infotech.monash.edu.au
Sun Sep 28 21:46:06 EDT 2008
>> I'm using the following code to access the "ORGANISM" tag value for the
>> record NC_002526.
>> I get a value of 0 even though the ORGANISM tag has a value. Any idea
>> this might be corrected?
>> my $des= $seq->get_tag_values("ORGANISM");
> You want the species object ($seq->species) -- see the Seq HOWTO, much of
> the Seq API is explained.
Of course Jason is correct here but there was still a semantic bug in
your code anyway which you should probably be aware of.
$seq->get_tag_values() returns an ARRAY which you are trying to store
in a SCALAR ($des). An array, in a scalar context, returns the SIZE of
the array, which in your case was zero (0) as there were no ORGANISM
tags. What you probably meant was:
my($des) = $seq->get_tag_values("ORGANISM");
my $des = ($seq->get_tag_values("ORGANISM")) [ 0 ];
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University
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