[Bioperl-l] Problem in OMIM parser

neeti somaiya neetisomaiya at gmail.com
Tue Dec 2 00:54:14 EST 2008


I am downloading the OMIM genemap file from here :


I was using the OMIMparser all these days to parse the genemap and omim.txt
files and get the relevant data, and it was working perfect, but today
suddenly I got an exception at the following line of my code :

 my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new(-genemap  =>
$genemap,-omimtext => $omimtext);

The exception I got was :

------------- EXCEPTION  -------------
MSG: Gene map file "genemap" is not in the expected format
STACK Bio::Phenotype::OMIM::OMIMparser::_read_genemap
STACK Bio::Phenotype::OMIM::OMIMparser::genemap_file_name
STACK Bio::Phenotype::OMIM::OMIMparser::new
STACK main::main parseOmimData.pl:56
STACK toplevel parseOmimData.pl:39


Please suggest what I can do now.

Even my blood says, B positive

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