[Bioperl-l] Blast parsers missing functions

Chris Fields cjfields at uiuc.edu
Thu Mar 22 13:56:16 EDT 2007


You can certainly add this as an enhancement request in Bugzilla, but  
unless someone codes for it we can't promise you when it would be  
added in.

chris

On Mar 22, 2007, at 10:25 AM, Kevin Brown wrote:

> I was looking through the deobfuscator after creating a blast file
> parser that failed on parsing a blast XML file due to a missing method
> and I see there are actually quite a few missing.
>
> Found in Bio::SearchIO::blast, but not Bio::SearchIO::blastxml or
> Bio::SearchIO::blasttable
> best_hit_only
> check_all_hits
> inclusion_threshold
> max_significance
> min_query_length
> min_score
> signif
>
> I use the min_score in my parser so that blastall can be run with a  
> high
> E and later filtered, or refiltered for other things after the  
> blast is
> done.
>
> It would be nice if all the blast parsers had most of these missing
> functions to at least keep them consistent with each other for parsing
> blast reports :)




More information about the Bioperl-l mailing list