[Bioperl-l] URGENT : Problem in OMIM parser

Chris Fields cjfields at uiuc.edu
Thu Aug 2 13:51:27 EDT 2007


Neeti,

The genemap wasn't loaded in all cases; don't know what the reasoning  
for it was, but it is fixed in CVS now  
(Bio::Phenotype::OMIM::OMIMparser, specifically).  I would recommend  
that you install a full upgrade to at least bioperl 1.5.2 before  
using this; I can't guarantee it will work with bioperl 1.4.

chris

On Aug 2, 2007, at 8:00 AM, neeti somaiya wrote:

> Also,
> As per the following links we can fetch data from the genemap file  
> as well
> :-
> http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Phenotype/OMIM/ 
> OMIMparser.pm
>
> But when I am trying to do so in the exact manner as given in the  
> above
> link, I get no data. As in there are OMIM ids which are present in  
> both the
> omim.txt and genemap files, and for such cases when I parse and  
> fetch data,
> data from both files should be obtained, but I aint getting it.
>
> For eg. while running the attached script, for OMIM id 100790, I  
> get all
> data from omim.txt but the cytoposition, gene symbol etc from  
> genemap is not
> coming, though it is present in the genemap file.
>
> Please help me find what could be going wrong.
>
> On 8/2/07, neeti somaiya <neetisomaiya at gmail.com> wrote:
>>
>> Hi,
>>
>> The script is attached with this mail.
>> I am using bioperl-1.4.
>>
>> Regards,
>> Neeti.
>>
>> On 8/1/07, Chris Fields < cjfields at uiuc.edu> wrote:
>>>
>>> Neeti,
>>>
>>> Only post to one list email address, namely the one I'm  
>>> responding to
>>> and the one shown here:
>>>
>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>>> The others are aliases so you essentially posted three times.  As  
>>> for
>>> your question: there was no attached script or any additional
>>> information (bioperl version would have also been nice), so we can't
>>> help you until we have something more to work with.
>>>
>>> chris
>>>
>>> On Aug 1, 2007, at 6:28 AM, neeti somaiya wrote:
>>>
>>>> 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
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>
>>
>> --
>> -Neeti
>> Even my blood says, B positive
>>
>>
>
>
> -- 
> -Neeti
> Even my blood says, B positive
> <parse_omim_original.pl>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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