[Bioperl-l] Problem Parsing BLAST output

[Ben Saville]

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
>
>
>
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