[Bioperl-l] URGENT : Problem in OMIM parser

Chris Fields cjfields at uiuc.edu
Wed Aug 1 15:02:07 UTC 2007


Only post to one list email address, namely the one I'm responding to  
and the one shown here:


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.


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

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