[Bioperl-l] URGENT : Problem in OMIM parser

Chris Fields cjfields at uiuc.edu
Thu Aug 2 14:16:56 EDT 2007


Neeti,

Keep this on the list please.  I am unable to reproduce this using  
your script with or without using the optional genemap file.  You  
really should upgrade bioperl to 1.5.2 and try the fix first; this is  
something that may have been fixed post-bioperl 1.4.

chris

On Aug 2, 2007, at 12:57 PM, neeti somaiya wrote:

> Waiting for your reply on the exception I had mentioned in my first  
> mail.
>
> Thanks.
>
> ---------- Forwarded message ----------
> From: neeti somaiya < neetisomaiya at gmail.com>
> Date: Aug 2, 2007 11:50 AM
> Subject: Re: [Bioperl-l] URGENT : Problem in OMIM parser
> To: bioperl-l at lists.open-bio.org
>
> Hi,
>
> The script is attached with this mail.
> I am using bioperl-1.4.
>
> Regards,
> Neeti.
>
>
> On 8/1/07, Chris Fields < cjfields at uiuc.edu> wrote:Neeti,
>
> Only post to one list email address, namely the one I'm responding to
> and the one shown here:
>
> http://bioperl.org/mailman/listinfo/bioperl-l
>
> The others are aliases so you essentially posted three times.  As for
> your question: there was no attached script or any additional
> information (bioperl version would have also been nice), so we can't
> help you until we have something more to work with.
>
> chris
>
> On Aug 1, 2007, at 6:28 AM, neeti somaiya wrote:
>
> > I have downloaded the omim.txt file from NCBI ftp site and I am
> > running my
> > attached parser on this file, the parser run stops in between with
> > this :-
> >
> > ------------- EXCEPTION  -------------
> > MSG: a part/organism must be assigned
> > STACK Bio::Phenotype::OMIM::OMIMentry::add_clinical_symptoms
> > /usr/lib/perl5/site_perl/5.8.8/Bio/Phenotype/OMIM/OMIMentry.pm:566
> > STACK Bio::Phenotype::OMIM::OMIMparser::_finer_parse_symptoms
> > /usr/lib/perl5/site_perl/5.8.8/Bio/Phenotype/OMIM/OMIMparser.pm:555
> > STACK Bio::Phenotype::OMIM::OMIMparser::_createOMIMentry
> > /usr/lib/perl5/site_perl/5.8.8/Bio/Phenotype/OMIM/OMIMparser.pm:536
> > STACK Bio::Phenotype::OMIM::OMIMparser::next_phenotype
> > /usr/lib/perl5/site_perl/5.8.8/Bio/Phenotype/OMIM/OMIMparser.pm:272
> > STACK toplevel parse_omim_original.pl:47
> >
> > --------------------------------------
> >
> > What is the reason for this?
> > Can anyone guide me please.
> >
> > --
> > -Neeti
> > Even my blood says, B positive
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
> -- 
> -Neeti
> Even my blood says, B positive
>
>
>
> -- 
> -Neeti
> Even my blood says, B positive
> <parse_omim_original.pl>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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