[Bioperl-l] URGENT : Problem in OMIM parser

neeti somaiya neetisomaiya at gmail.com
Wed Aug 1 07:28:40 EDT 2007


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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