1 Aug 2007 13:28
URGENT : Problem in OMIM parser
neeti somaiya <neetisomaiya <at> gmail.com>
2007-08-01 11:28:40 GMT
2007-08-01 11:28:40 GMT
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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