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

[Brian Osborne]

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
> 
> 
> 
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