[Bioperl-l] getting/setting species names with Bio::Species
David.Messina at sbc.su.se
Fri Jan 15 13:37:17 EST 2010
Well, looks like I ignored the deprecation warnings at my own peril. :)
I'll reimplement my code using Bio::Taxon directly instead. I made a little test using the node_name() method as Chris suggested, and it seems to do the trick nicely.
> If that's really what the documentation says, it's wrong.
I'm afraid so. In the POD
> Title : species
> Usage : $self->species( $species );
> $species = $self->species();
> Function: Get or set the scientific species name.
> Example : $self->species('Homo sapiens');
> Returns : Scientific species name as string
> Args : Scientific species name as string
and the HOWTO
> # legible and long
> my $species_object = $seq_object->species;
> my $species_string = $species_object->species;
> # Perlish
> my $species_string = $seq_object->species->species;
> # either way, $species_string is "Homo sapiens"
Unless there's objection, I'll fix both of those.
> It is the binomial() method that does this (as getter and setter).
Great, thanks for the clarification, Hilmar.
More information about the Bioperl-l