[Bioperl-l] Re: [Bioperl-guts-l] Difficulty to recover the OS line
james.wasmuth at ed.ac.uk
Fri Apr 9 08:14:55 EDT 2004
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...
Laure Quintric wrote:
> 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.
> 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.
>> Laure Quintric wrote:
>>> 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 Quintric
>>> Trainee At the Biologic Station of Roscoff
>>> E-mail : Quintric at sb-roscoff.fr
>>> Bioperl-guts-l mailing list
>>> Bioperl-guts-l at portal.open-bio.org
>> "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
EH9 3JT |
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