[Bioperl-l] Fast BLAST parsing

Chris Fields cjfields at illinois.edu
Tue Oct 28 10:40:52 EDT 2008


Never tried it to be honest, but I can see where that would be  
helpful.  It would probably require a bit of I/O magic (checking file  
position before/after parse, finding the query, etc) but I think it's  
a possibility.

You can always add this in as an enhancement request to Bugzilla;  
patches are also welcome!

chris

On Oct 28, 2008, at 8:37 AM, Adam Witney wrote:

>
> Just wondering, could Bio::Index::Blast be used to generate the  
> Index as the BLAST is performed, say with  
> Bio::Tools::Run::StandAloneBlast?
>
> thanks
>
> adam
>
> On 23 Oct 2008, at 18:09, Chris Fields wrote:
>
>> Could you index the BLAST report using Bio::Index::Blast?  From the  
>> synopsis:
>>
>>   use Bio::Index::Blast;
>>   my ($indexfile,$file1,$file2,$query);
>>   my $index = Bio::Index::Blast->new(-filename => $indexfile,
>> 				       -write_flag => 1);
>>   $index->make_index($file1,$file2);
>>
>>   my $data = $index->get_stream($query);
>>
>>   my $blast_report = $index->fetch_report($query);
>>   print "query is ", $blast_report->query, "\n";
>>   while ( my $result = $blast_report->next_result ) {
>>           print $result->algorithm, "\n";
>>           while ( my $hsp = $result->next_hit ) {
>>             print "\t name ", $hsp->name,
>>           }
>>           print "\n";
>>   }
>>
>> I think you can index using a callback on the query name (so you  
>> can look up by various means).
>>
>> chris
>>
>>
>> On Oct 23, 2008, at 11:22 AM, Brian Osborne wrote:
>>
>>> Bioperl,
>>>
>>> I'm not familiar with the very latest and greatest in BLAST  
>>> parsing, perhaps you can help me here. I have a large Blast output  
>>> file, it has multiple results in it. I'd like to rapidly find the  
>>> relevant result for a given query name, I don't want to iterate  
>>> over the results checking for query_name() each time. How can I  
>>> directly pull out a result using query name?
>>>
>>>
>>> Thanks again,
>>>
>>> Brian O.
>>> --
>>> Brian Osborne, PhD
>>> BioTeam: http://bioteam.net
>>> email: briano at bioteam.net
>>> mobile: 978-317-3101
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Marie-Claude Hofmann
>> College of Veterinary Medicine
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
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>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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