[Bioperl-l] Problem in OMIM parser

[neeti somaiya]

Hey,

I ran my parser again today, with no changes what so ever (I did not check
for the line break or anything), and it ran fine.

~Neeti.

On Sat, Dec 6, 2008 at 11:50 AM, Mark A. Jensen <maj at fortinbras.us> wrote:

> 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
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>



-- 
-Neeti
Even my blood says, B positive