[Bioperl-l] Fast BLAST parsing

Adam Witney awitney at sgul.ac.uk
Tue Oct 28 09:37:23 EDT 2008


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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