[Bioperl-l] Behavior of Bio::Species object

[Ewan Birney]

On Sun, 20 Oct 2002, Michael Muratet wrote:

> Greetings
>
> In processing GenBank files which I then write out in EMBL format, the
> OS tag in the EMBL file carries information that was in the SOURCE tag
> of the GenBank file. For example, using mouse.gbff, the SOURCE line
> lists "house mouse" and the ORGANISM line below it gives Mus musculus
> followed by the rest of the classification. If I initialize the species
> field in a Bio::Seq object with the species object obtained from a
> GenBank file and then write it out in EMBL format, the OS tag line will
> say "Mus musculus (house mouse)". Wouldn't it be better just to have the
> binomial species name? Should I always expect information after the
> binomial name and parse off the first two words?

Michael - you are seeing the hard end of trying to get bioperl to work -
we want to normalise information but also want to as close as possible
"round trip" (recreate exactly) the flat files and have all the
information to hand.

As it happens, on the species object I believe there is the method
"binomial_name" which gives the genus species from the classification, not
parsing the common name slot

I think Hilmar suggested a new slot coming into Bio::Species to handle
more of this.



>
> Thanks.
>
> Mike
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