[Bioperl-l] Fast BLAST parsing

Brian Osborne bosborne11 at verizon.net
Fri Oct 24 08:47:21 EDT 2008


Chris,

Here I am thinking there's some fancy new approach but it's the old  
standby that does the trick!

Also corrected that Synopsis, it didn't work for me.

Thanks again,

Brian O.

On Oct 23, 2008, at 1:09 PM, 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
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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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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