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

[Hubert Prielinger]

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