Re: [GUSDEV] Re: ISF errors list

[Steve F. <sfi...@pc...>]

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="ESAG1"
>           primer_bind     1..11
>                           /gene="ESAG1"
>           exon            <12..21
>                           /gene="ESAG1"
>                           /note="min-exon"
>           CDS             25..>447
>                           /gene="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... <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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