[Bioperl-l] Problem Parsing BLAST output

[Chris Fields]

Just in case anyone needs it, there is a way to index these as well (both BLAST and the two tabular BLAST versions) for fast lookups of specific reports, if needed.  See Bio::Index::Blast and Bio::Index::BlastTable in BioPerl.

Caveat: I believe there is a bug with BLAST+ text output indexing (it chops the header off subsequent reports).  I haven't investigated it enough, though, but I'll try looking into it today.  

chris

On Aug 24, 2010, at 10:35 AM, Ben Saville wrote:

> Sorry for the Delay in replying, 454 data analysis is very time consuming.
> 
> please see http://seqanswers.com/forums/showthread.php?t=6484
> For a discussion about this problem, and how we solved the issue.
> 
> Thanks for the reply though, much appreciated!
> 
> Regards
> Ben Saville
> 
> 
> 
> 
> 
> On 20 Aug 2010, at 14:48, Dave Messina wrote:
> 
>> Hi Ben,
>> 
>> I would not use the script you posted — I don't think it does what you want.
>> 
>> If you haven't already, you should take a look at the beginners' HOWTO
>> 
>> 	http://www.bioperl.org/wiki/HOWTO:Beginners
>> 
>> 
>> the SearchIO HOWTO
>> 
>> 	http://www.bioperl.org/wiki/HOWTO:SearchIO
>> 
>> 
>> and the example scripts included with BioPerl:
>> 
>> 	http://www.bioperl.org/wiki/Scripts
>> 
>> 
>> 
>> Incidentally, it's a lot of fiddly data processing to parse blast reports for many contigs against multiple databases and then go back and collate the results by query. I'm not sure exactly what you want to do once you've separated by query — if you provide some more information, we could suggest ways to best get you where you want to go.
>> 
>> I will mention, though, that BLAST has the ability to search multiple separate databases in one go and collate the results for you. So that's something to consider.
>> 
>> 
>> 
>> Dave
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l