[Bioperl-l] load_seqdatabase error with a specific locus from genbank
cjfields at illinois.edu
Tue Apr 7 01:32:52 EDT 2009
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/
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"
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l