[Bioperl-l] load_seqdatabase error with a specific locus from genbank

[Hilmar Lapp]

On Apr 8, 2009, at 11:35 PM, Hilmar Lapp wrote:

>
> On Apr 8, 2009, at 11:29 AM, Johann PELLET wrote:
>
>> [...]
>> and finally EU608407 and EU608559  made a crash:
>>
>> [...]
>> --------------------- WARNING ---------------------
>> MSG: Unexpected error in feature table for  Skipping feature,  
>> attempting to recover
>> ---------------------------------------------------
>> #######...14 times ...############
>
> I would assume that you figured out that this was triggered by or  
> affected EU608407? Would you mind sharing how?

Looking at EU608407, it most likely wasn't the culprit or stumbling  
stone. It must have been triggered before that.

> [...]
> So are there other sequences associated with that PubMed ID?

To answer my own question, it's indeed EU608407 that's from the same  
PubMed ID, and so am I correct in assuming that you didn't get the  
exception for that record, which would mean that the reference was  
properly inserted when that sequence was loaded.

The second occurrence of the same PubMed ID should have actually  
triggered a successful lookup of the previously inserted record, which  
would then have skipped the insert. The fact that that didn't happen  
suggests that the PubMed ID also wasn't properly extracted from the  
Genbank record. So my first suspicion remains that your file is  
corrupted.

Otherwise, if you download this record:
http://www.ncbi.nlm.nih.gov/nuccore/183191257

in GenBank format and try to load it alone, it should yield the same  
error. Can you indeed reproduce the problem in that way?

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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