Re: [GUSDEV] Re: ISF errors list

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

Steve,

  We have a GenBank file with 1.5GB and to fix all issues that we find
manually becomes a very cost task, because we do not have as much time.  Do
you have plans to improve the ISF in this direction?

Ricardo

On 3/7/06, Steve Fischer <sfi...@pc...> wrote:
>
> ISF does not now support any way to ignore a GI.
>
> so, for now, copy the genbank to file to a .fixed version, and fix the
> problem, either by removing the GI or by tweeking the feaatures
>
> steve
>
> Ricardo Balbi wrote:
>
> > Ok Aaron, but what we have to do ? edit the GenBank file? ignore this
> > GI? if yes, how to ignore?
> >
> > On 2/16/06, *Aaron J. Mackey* < am...@pc...
> > <mailto:am...@pc...>> wrote:
> >
> >
> >
> >     On Feb 17, 2006, at 6:58 PM, davila wrote:
> >
> >     > 3. 102829.txt - Apparently a BioPerl error
> >     > A 102829.gb <http://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 a=
t
> >     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... <mailto: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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