[Bioperl-l] parse Blast Output and Composition Based Statisticsparameter

[Hubert Prielinger]

Hello Barry,
Thanks, but I have already solved it, as I have respondet to Jason, the 
parameter doesn't work with yes or no, anymore, because after contacting 
the NCBI
helpdesk, they figured out that you have to use '0' or '1', because they 
have recently changed it
like:
$Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'} = '1';

with me, it didn't work with 'yes' or  'no'

regards
Hubert

PS: orginal response mail by NCBI helpdesk:

Hello,

I'm sorry, this has recently changed. Instead of "Yes", try using either
'0' '1' or '2', where:

'0' = No Composition-based statistics
'1' = Conditional compositional score matrix adjustment (apply only to
'biased' sequences)
'2' = Universal compositional score matrix adjustment (apply to all).

This works with the URLAPI; I've not tested with the perl module.

Best regards,
Wayne


Barry Moore wrote:

>Hubert,
>
>What exactly isn't working for you with the composition based
>statistics.  Are you getting different e-values from Bioperl vs. NCBI
>website.  It seems to be working OK for me (at least on one quick test).
>
>Barry
>
>  
>
>>-----Original Message-----
>>From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>>bounces at portal.open-bio.org] On Behalf Of Jason Stajich
>>Sent: Monday, January 16, 2006 6:12 PM
>>To: bioperl-ml List
>>Cc: Hubert Prielinger
>>Subject: Fwd: [Bioperl-l] parse Blast Output and Composition Based
>>Statisticsparameter
>>
>>sorry - i don't really have the time to support this module - lots of
>>people on the list use it so they can hopefully help.
>>
>>Begin forwarded message:
>>
>>    
>>
>>>From: Hubert Prielinger <hubert.prielinger at gmx.at>
>>>Date: January 16, 2006 3:45:21 PM EST
>>>To: Jason Stajich <jason.stajich at duke.edu>
>>>Subject: Re: [Bioperl-l] parse Blast Output and Composition Based
>>>Statistics parameter
>>>
>>>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
>>>
>>>      
>>>
>>--
>>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
>>    
>>
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