[Bioperl-l] load_seqdatabase error with a specific locus from genbank
johann.pellet at inserm.fr
Tue Apr 7 04:48:56 EDT 2009
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
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
> 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:
>>> order(location,location, ... location)
>>> The elements can be found in the specified order (5' to 3'
>>> 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"
>> gene order(S67862.1:72..75,join(S67863.1:1..788,1..19))
>> gene 55..>77
>> /gene="fusion glycoprotein F"
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>> Bioperl-l at lists.open-bio.org
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