Re: [GUSDEV] Re: ISF errors list

[Ricardo B. <rb...@gm...>]

Ok Aaron, but what we have to do ? edit the GenBank file? ignore this GI? i=
f
yes, how to ignore?

On 2/16/06, Aaron J. Mackey <am...@pc...> wrote:
>
>
>
> On Feb 17, 2006, at 6:58 PM, davila wrote:
>
> > 3. 102829.txt - Apparently a BioPerl error
> > A 102829.gb file is an example
>
> Read the error message, it tells you exactly what is wrong:
>
> ------------- EXCEPTION  -------------
> MSG: 1 there is a conflict with exons; there was an explicitly stated
> exon with location 12..21, yet I cannot generate this e
> xon from the supplied mRNA locations
> 1 There are some inferred exons that are not in the explicit exon
> list; they are the exons at locations:
> 25..447
>
> STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /usr/lib/
> perl5/site_perl/5.8.6/Bio/SeqFeature/Tools/Unflattener.pm:1
> 606
> ...
>
>
> Then look at the GenBank file:
>
>       gene            1..447
>                       /gene=3D"ESAG1"
>       primer_bind     1..11
>                       /gene=3D"ESAG1"
>       exon            <12..21
>                       /gene=3D"ESAG1"
>                       /note=3D"min-exon"
>       CDS             25..>447
>                       /gene=3D"ESAG1"
>
> I have to agree with the Unflattener, this doesn't make any sense at
> all.
>
> Garbage in, garbage out.
>
> -Aaron
>
>
> --
> Aaron J. Mackey, Ph.D.
> Project Manager, ApiDB Bioinformatics Resource Center
> Penn Genomics Institute, University of Pennsylvania
> email:  am...@pc...
> office: 215-898-1205 (Biology, 212 Goddard Labs)
>          215-746-7018 (PCBI, 1428 Blockley Hall)
> fax:    215-746-6697 (Penn Genomics Institute)
> postal: Penn Genomics Institute
>          Goddard Labs 212
>          415 S. University Avenue
>          Philadelphia, PA  19104-6017
>
>
>
>
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