[Bioperl-l] Re: [Bioperl-guts-l] Difficulty to recover the OS line in Swissprot

[James Wasmuth]

Laure,

I started a thread a few weeks back when I was sorting out this issue in 
genbank.  No-one really joined in so I went a head and did as I saw fit.

What do you expect to get from bionomial?  The way I'll fix it is to 
return "Unknown prokaryotic organism" from $seq->species()->binomial().

If you think it should ouput something else then I'm open to suggestions...

-james



Laure Quintric wrote:

> James,
>
> OK, I'm reassured  not to be the only one with that problem, and 
> knowing a solution will be given is good. Don't forget to tell me when 
> you will get it, I really need to use that functionality ! Thanks.
>
> Laure.
>
>
> A 11:04 09/04/2004 +0100, vous avez écrit :
>
>> Hi Laure,
>>
>> This is a problem I encountered with genbank entries.  I submitted a 
>> fix for that one and will get it sorted on the swiss.pm and embl.pm 
>> shortly.  Bank Holiday today so away.  Hopefully on Monday.
>>
>> -james
>>
>>
>>
>>
>>
>> Laure Quintric wrote:
>>
>>> Hello,
>>>
>>> I've remarked that when the OS line in Swissprot database is like 
>>> "OS   Unknown prokaryotic organism." ,
>>> it's impossible to recover a vacuum variable or a variable in which 
>>> is written "Unknown prokaryotic organism".
>>> Because when I launch my algorythm on the protein called "DHE4_UNKP"
>>>
>>>     use Bio::Species;
>>>     #species (species_name OS line)
>>>     my $species_name = $seq->species()->binomial();
>>>     print $species_name."\n";
>>>
>>> it returns
>>>
>>> "Can't call method binomial on an undefined value"
>>>
>>> Have you got a solution to resolve this problem ??
>>>
>>> Thx !
>>>
>>> Laure.
>>> -----
>>> Laure Quintric
>>> Trainee At the Biologic Station of Roscoff
>>> CNRS
>>> France
>>> E-mail : Quintric at sb-roscoff.fr
>>>
>>> _______________________________________________
>>> Bioperl-guts-l mailing list
>>> Bioperl-guts-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
>>
>>
>>
>> -- 
>> "There are some days when I think I'm going to die from an overdose 
>> of satisfaction."
>>              --- Salvador Dali
>>
>> Nematode Bioinformatics          |
>> Blaxter Nematode Genomics Group  |
>> School of Biological Sciences    |
>> Ashworth Laboratories            | tel: +44 131 650 7403
>> University of Edinburgh          | web: www.nematodes.org
>> Edinburgh                        |
>> EH9 3JT                          |
>> UK                               |
>
>
>

-- 
"There are some days when I think I'm going to die from 
an overdose of satisfaction."
	     --- Salvador Dali

Nematode Bioinformatics          |
Blaxter Nematode Genomics Group  |
School of Biological Sciences    |
Ashworth Laboratories            | tel: +44 131 650 7403
University of Edinburgh          | web: www.nematodes.org
Edinburgh                        |
EH9 3JT                          |
UK                               |