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

[Chris Fields]

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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