[Bioperl-l] parse long organism name

[Hilmar Lapp]

To be honest I'm not even sure what binomial is supposed to return 
here. The problem originates from the fact that binomial, species, and 
genus won't store their values redundantly but rather access the 
classification array (kingdom->order->blah->foo etc) at the expected 
locations. common_name on the contrary does store it's value itself.

I don't feel I'm suited to take this on. If anybody else does please 
don't hesitate to come forward. My gut reaction would be to push more 
towards using the taxonomy classes by Jason et al over the Bio::Species 
class. I'd hope that model would be able to handle such weirdnesses 
better.

	-hilmar

On Monday, January 3, 2005, at 10:08  AM, Qunfeng wrote:

> I didn't get any error msg.
>
> When I parse the organism name with the following methods:
>
> my $organism = $seq_object->species->binomial();
> my $species = $seq_object->species->species();
> my $genus = $seq_object->species->genus();
> my $common_name = $seq_object->species->common_name();
>
> I got the following value
>
> $organism as Paphiopedilum 'Dark
> $species as   Paphiopedilum
> $genus as 'Dark
> $common_name as  Paphiopedilum 'Dark Roller' x Paphiopedilum 
> rothschildianum
>
> So, the common_name is correct, while binmial(), species(), and 
> genus() all assume that the name is in CORRECT species, genus form.
>
> Qunfeng
>
> At 10:14 AM 12/17/2004, Hilmar Lapp wrote:
>> What's the error that you get, if any?
>>
>>         -hilmar
>>
>> On Thursday, December 16, 2004, at 03:00  PM, Qunfeng wrote:
>>
>>> For example,
>>> http://www.ncbi.nlm.nih.gov/entrez/ 
>>> viewer.fcgi?db=nucleotide&val=47776109
>>>
>>> It has a LONG name:
>>> <http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/ 
>>> wwwtax.cgi?id=232838>Paphiopedilum 'Dark Roller' x Paphiopedilum
>>> rothschildianum
>>>
>>> Is there anyway in Bioperl to parse out that long name from GenBank
>>> format file?
>>>
>>> Thanks!
>>>
>>> Qunfeng _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> --
>> -------------------------------------------------------------
>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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