[Bioperl-l] parse Blast Output and Composition Based Statistics parameter

[Hubert Prielinger]

Hi Brian,
yes, I have tried pasting the sequence manually at the NCBI Homepage and 
it is working fine.

regards
Hubert


Brian Osborne wrote:

>Hubert,
>
>If all the other parameters are passed correctly then I suspect this is not
>a BioPerl problem. Did you try manually pasting these URLs into the browser
>to confirm that NCBI is processing the parameters correctly?
>
>Brian O.
>
>
>On 1/16/06 4:44 PM, "Hubert Prielinger" <hubert.prielinger at gmx.at> wrote:
>
>  
>
>>Hubert Prielinger wrote:
>>
>>    
>>
>>>Jason Stajich wrote:
>>>
>>>      
>>>
>>>>(please don't try and post to bioperl-announce, it is not for
>>>>questions.)
>>>>
>>>>On Jan 12, 2006, at 6:57 PM, Hubert Prielinger wrote:
>>>>
>>>>        
>>>>
>>>>>Hello,
>>>>>I want to know, if there is a possibility to get from a Blast
>>>>>Outputfile the whole Sequence of a protein not only the best local
>>>>>alignment...
>>>>>for example:
>>>>>
>>>>>          
>>>>>
>>>>No. The parser can only return to you what is in the report file...
>>>>use Bio::DB::GenPept to retrieve the sequence via the web or
>>>>(recommended) use a locally indexed sequence database like
>>>>Bio::DB::Fasta
>>>>
>>>>        
>>>>
>>>>>>ref|XP_480077.1| hypothetical protein [Oryza sativa (japonica
>>>>>>            
>>>>>>
>>>>>cultivar-group)]
>>>>>dbj|BAD33542.1| hypothetical protein [Oryza sativa (japonica
>>>>>cultivar-group)]
>>>>>        Length=95
>>>>>
>>>>>Score = 24.1 bits (47),  Expect =   493
>>>>>Identities = 6/7 (85%), Positives = 7/7 (100%), Gaps = 0/7 (0%)
>>>>>
>>>>>Query  2   KKRRRWW  8
>>>>>               K+RRRWW
>>>>>Sbjct  87  KRRRRWW  93
>>>>>
>>>>>and now, if I parse the file, I want to get the whole Sequence of
>>>>>this hypothetical protein....is that possible with hsp for example,
>>>>>or any other way....
>>>>>
>>>>>my second question is:
>>>>>I do my blast search with bioperl and the remoteblast
>>>>>module.....each parameter is working very well, except the
>>>>>composition based statistics parameter....
>>>>>it looks like that:
>>>>>
>>>>>my $factory = $Bio::Tools::Run::RemoteBlast::HEADER
>>>>>{'COMPOSITION_BASED_STATISTICS'} = 'yes';
>>>>>
>>>>>          
>>>>>
>>>>uh no that is not how you would do it.
>>>>You can make it the default for any factories you use in the script
>>>>by doing this
>>>>
>>>>        
>>>>
>>>>>$Bio::Tools::Run::RemoteBlast::HEADER
>>>>>{'COMPOSITION_BASED_STATISTICS'} = 'yes';
>>>>>          
>>>>>
>>>>then
>>>>$factory = Bio::Tools::Run::RemoteBlast->new();
>>>>
>>>>
>>>> =OR=
>>>>Once you have a factory object you can set the parameter explicitly:
>>>>$factory->submit_parameter('COMPOSITION_BASED_STATISTICS', 'yes');
>>>>
>>>>        
>>>>
>>>>>it should work like that, but it doesn't....
>>>>>
>>>>>Thanks for your help in advance......
>>>>>
>>>>>regards
>>>>>Hubert
>>>>>_______________________________________________
>>>>>Bioperl-l mailing list
>>>>>Bioperl-l at portal.open-bio.org
>>>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>>          
>>>>>
>>>>
>>>>-- 
>>>>Jason Stajich
>>>>Duke University
>>>>http://www.duke.edu/~jes12
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at portal.open-bio.org
>>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>        
>>>>
>>Hi Jason,
>>I have tried everything that you suggested, but the Composition Based
>>Statistic parameter isn't still working, every
>>other parameter works using e.g
>>
>>$Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = '1000';
>>
>>thanks in advance
>>Hubert
>>
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>    
>>
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