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

[Johann PELLET]

Thanks all,

I will update bioperl-live using svn right now, and I will restart to  
load sequences  into my biosql database.
Hilmar, My GenBank file contains only virus sequences. I downloaded it  
using eutils, (db=nuccore, tool=ebot, rettype=gb ...).

Thank you again

-- --

Johann Pellet


Le 7 avr. 09 à 07:32, Chris Fields a écrit :

> Fixed in svn now and have added this as a test case (passes all  
> tests in bioperl-live).  For some reason this wasn't catching some  
> more complex combinations of operators, mainly those with mixes of  
> order/join.
>
> chris
>
> On Apr 6, 2009, at 10:59 PM, Chris Fields wrote:
>
>> On Apr 6, 2009, at 8:05 PM, Torsten Seemann wrote:
>>
>>>> The full record is here: http://www.ncbi.nlm.nih.gov/nuccore/544772
>>>
>>> gene            order(S67862.1:72..75,join(S67863.1:1..788,1..19))
>>>
>>>> Does anyone see why the location parser should have a problem  
>>>> with the first
>>>> gene feature? It's nested, and has remote location components,  
>>>> but at first
>>>> sight nothing jumps out at me as extraordinary. Has someone  
>>>> recently changed
>>>> the location parsing code? If no-one has an immediate idea what  
>>>> could be at
>>>> work here, this needs investigating.
>>
>> The location parsing code was refactored above 3-4 years ago w/o  
>> problems.  This'll be the first one to crop up.  I'll try taking a  
>> look at it.
>>
>>> I'm not sure if Bioperl handles the order() operator?
>>>
>>> For those unfamilair with the order() operator:
>>>
>>> http://www.ncbi.nlm.nih.gov/collab/FT/#3.5.2
>>>
>>> order(location,location, ... location)
>>> The elements can be found in the specified order (5' to 3'  
>>> direction),
>>> but nothing is implied about the reasonableness about joining them.
>>>
>>>
>>> --Torsten Seemann
>>> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
>>> University, AUSTRALIA
>>
>> It's interesting that the version from eutils differs significantly  
>> in the feature table when retrieving 'gb' or 'gbwithparts', the  
>> latter resolves the location (see below).  Regardless we'll need to  
>> make sure this is parseable.
>>
>> ....
>>
>> FEATURES             Location/Qualifiers
>>    source          1..77
>>                    /organism="Ovine respiratory syncytial virus"
>>                    /mol_type="genomic RNA"
>>                    /db_xref="taxon:28869"
>>    gene            order(S67862.1:72..75,join(S67863.1:1..788,1..19))
>>                    /gene="G"
>>    gene            55..>77
>>                    /gene="fusion glycoprotein F"
>>
>>
>>
>> chris
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>