[Bioperl-l] URGENT : Problem in OMIM parser

neeti somaiya neetisomaiya at gmail.com
Fri Aug 3 01:46:32 EDT 2007


Hi,

Thanks a lot.
The exception is not coming after upgrade to bioperl-1.5.2
But the genemap data is still a problem.

You had mentioned that I should take Bio::Phenotype::OMIM::OMIMparser,
specifically from cvs. Where exactly can I get it?

Thanks,
Neeti.

On 8/2/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
> 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
>
>
>
>


-- 
-Neeti
Even my blood says, B positive


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