[Bioperl-l] Problem in OMIM parser

[Mark A. Jensen]

Hi Neeti - 

I looked at the source, and found that that exception is thrown 
when there are not exactly 18 fields ( separated by 17 "|" symbols ) 
on a genemap file line. The Bioperl tests ran fine for OMIMparser 
on the test data file. I had a hunch, so I removed the final linebreak 
from the test file; that is, from this...
.
.
.
1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, ...[\n]
1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibi...[\n]
1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration sit...[\n]
1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducibl...[\n]
[EOF]

to this...
.
.
.
1.132|12|2|97|1p35.1|P28|P|Inner dynein arm, clamydomonas, ...[\n]
1.133|6|10|98|1p35|BAI2|P|Brain-specific angiongenesis inhibi...[\n]
1.134|8|21|91|1p35|EBVS1|P|Epstein-Barr virus integration sit...[\n]
1.135|3|21|93|1p35|G1P3, IFI616|C|Interferon, alpha-inducibl...[EOF]

and ran the test again. Immediately, I got

**
ok 1 - use Bio::Phenotype::OMIM::OMIMparser;

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Gene map file "t\data\omim_genemap_test" is not in the expected format
STACK: Error::throw
STACK: Bio::Root::Root::throw c:/Perl/site/lib/Bio/Root/Root.pm:374
STACK: Bio::Phenotype::OMIM::OMIMparser::_read_genemap c:/Perl/site/lib/Bio/Phen
otype/OMIM/OMIMparser.pm:883
STACK: Bio::Phenotype::OMIM::OMIMparser::genemap_file_name c:/Perl/site/lib/Bio/
Phenotype/OMIM/OMIMparser.pm:408
STACK: Bio::Phenotype::OMIM::OMIMparser::new c:/Perl/site/lib/Bio/Phenotype/OMIM
/OMIMparser.pm:224
STACK: t/Phenotype/OMIMparser.t:16
-----------------------------------------------------------
# Looks like you planned 174 tests but only ran 1.
# Looks like your test died just after 1.
**

just your exception. So you might begin by making sure you're not chopping the final
newline character from your input files, or visiting those files to make sure there is 
a linebreak after the final line.

Hope this a start.
cheers MAJ