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

[Jason Stajich]

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