[Bioperl-l] Bio::SearchIO - Accessing Model parameters (score, evalue, description)

Selvi Kadirvel selvik at ufl.edu
Wed Jun 28 11:21:37 EDT 2006


Thanks for your reply Chris.

I am attaching a part of the report I am trying to parse.

Also I see that, Bio::SearchIO::hmmer.pm is parsing all three  
sections. I am not sure how (or whether) fields from Section 1 are  
actually being made available through Bio::SearchIO or Bio::Search:: 
[Hit | Hsp | Result].

I'll look into Bio::Tools::Hmmpfam and let you know if that works for  
me.

-Selvi


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On Jun 28, 2006, at 10:55 AM, Chris Fields wrote:

> I hate responding to myself!!  Forgot to add that there is also
> Bio::Tools::Hmmpfam :
>
> http://www.bioperl.org/wiki/Module:Bio::Tools::Hmmpfam
>
> I'll check if Bio::SearchIO catches this data and let you know what  
> I find
> out.  It should at least some according to the mapping.
>
> Chris
>
>> Selvi,
>>
>> Can you send me the report you are trying to parse as an  
>> attachment?  I'll
>> give it a look.
>>
>> Judging by the pdoc this is mapped for the event handler so it  
>> should be
>> there.  From the %MAPPING hash:
>>
>>                  'HMMER_program'   => 'RESULT-algorithm_name',
>>                  'HMMER_version'   => 'RESULT-algorithm_version',
>>                  'HMMER_query-def' => 'RESULT-query_name',
>>                  'HMMER_query-len' => 'RESULT-query_length',
>>                  'HMMER_query-acc' => 'RESULT-query_accession',
>>                  'HMMER_querydesc' => 'RESULT-query_description',
>>                  'HMMER_hmm'       => 'RESULT-hmm_name',
>>                  'HMMER_seqfile'   => 'RESULT-sequence_file',
>> 	           'HMMER_db'        => 'RESULT-database_name',
>>
>> Chris
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>> bounces at lists.open-bio.org] On Behalf Of Kadirvel, Selvi
>>> Sent: Tuesday, June 27, 2006 7:55 AM
>>> To: bioperl-l at lists.open-bio.org
>>> Cc: selvik at ufl.edu
>>> Subject: [Bioperl-l] Bio::SearchIO - Accessing Model parameters  
>>> (score,
>>> evalue, description)
>>>
>>> All,
>>>
>>> (I am new to Bioinformatics and Bioperl, so please apologize if I
>>> get my terminology wrong)
>>>
>>> I am currently using Bio::SearchIO to parse HMMPFAM reports. This
>>> report consists of three sections namely;
>>>
>>> 1. A ranked list of the best scoring HMMs
>>> 2. A list of the best scoring domains in order of their occurrence
>>> in the sequence
>>> 3. Alignments for all the best scoring domains.
>>>
>>> Section 3 can be truncated to a specific number using the ??A?
>>> option when building the report.
>>>
>>> Though the Bio::SearchIO::hmmer module parses through the entire
>>> HMMER report (Section 1, 2 and 3), the set of values made
>>> available through Bio::Search::Result::ResultI seem to be using
>>> Section 3 alone. So when we use the ?A option to truncate, we lose
>>> otherwise useful information in Section 1. This information is
>>> lost (only) for those models that do not have any of their domains
>>> in the top ?A number of? best scoring domains. The fields that are
>>> not available are:
>>>
>>> 1.	Description of a model
>>> 2.	Score of a model
>>> 3.	Evalue of a model
>>>
>>> If I use the older Bio::Tools::HMMER:Results module, NEITHER
>>> Bio::Tools::HMMER::Domain or Bio::Tools::HMMER::Set allow me to
>>> retrieve the above listed values. Scores and Evalues are available
>>> for each domain but not for the model it belongs to.
>>>
>>> I was wondering if there is any other method to access these
>>> values or do I have to write my own module to do this?
>>>
>>> Any ideas/suggestions would be greatly appreciated.
>>>
>>> Thank you!
>>>
>>>
>>>
>>>
>>> Selvi Kadirvel
>>>
>>> Graduate Research Assistant
>>> High Performance Computing Center
>>> University of Florida
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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>



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