[Bioperl-l] URGENT : Problem in OMIM parser

neeti somaiya neetisomaiya at gmail.com
Thu Aug 2 09:00:33 EDT 2007


Also,
As per the following links we can fetch data from the genemap file as well
:-
http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Phenotype/OMIM/OMIMparser.pm

But when I am trying to do so in the exact manner as given in the above
link, I get no data. As in there are OMIM ids which are present in both the
omim.txt and genemap files, and for such cases when I parse and fetch data,
data from both files should be obtained, but I aint getting it.

For eg. while running the attached script, for OMIM id 100790, I get all
data from omim.txt but the cytoposition, gene symbol etc from genemap is not
coming, though it is present in the genemap file.

Please help me find what could be going wrong.

On 8/2/07, neeti somaiya <neetisomaiya at gmail.com> wrote:
>
> 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
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