gusdev-gusdev

[GUSDEV] Re: ISF errors list

[Aaron J. M. <am...@pc...>]

On Feb 17, 2006, at 6:58 PM, davila wrote:

> 2. MSG: operator "gap" unrecognized by parser
> An gap.tar.gz file was created ana annexed containing several GIs  
> associated to this error.

This is a known (old) BioPerl error; GenBank has introduced/allowed a  
feature location operation called "gap()" (like "join()" or  
"complement()") that is not valid EMBL/GenBank/DDBJ feature-table  
syntax.  See:

   http://bugzilla.open-bio.org/show_bug.cgi?id=1319

This is fixed in BioPerl 1.5.1, I believe, and maybe even in 1.4

-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

Re: [GUSDEV] Re: ISF errors list

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

Hi Aaron,
  This problem still continue ... :(
  We are using BioPerl 1.5.1 and ISF with CVS revision 4573.

  Have you been tried to run ISF with those files sent to the list ?
  Do you have any other tips to us ?

Ricardo

On 2/16/06, Aaron J. Mackey <am...@pc...> wrote:
>
>
> On Feb 17, 2006, at 6:58 PM, davila wrote:
>
> > 2. MSG: operator "gap" unrecognized by parser
> > An gap.tar.gz file was created ana annexed containing several GIs
> > associated to this error.
>
> This is a known (old) BioPerl error; GenBank has introduced/allowed a
> feature location operation called "gap()" (like "join()" or
> "complement()") that is not valid EMBL/GenBank/DDBJ feature-table
> syntax.  See:
>
>    http://bugzilla.open-bio.org/show_bug.cgi?id=3D1319
>
> This is fixed in BioPerl 1.5.1, I believe, and maybe even in 1.4
>
> -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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