[Bioperl-l] blastxml !defined($hsp->significance)

Chris Fields cjfields at illinois.edu
Thu Feb 5 13:25:41 EST 2009


Dan,

This has been fixed in bioperl-live.  As mentioned it was a problem  
with significance() not checking defined-ness (it was merely checking  
bool).

The fix is available via svn, you only need one file (Bio/Search/HSP/ 
GenericHSP.pm).  It should be showing up via anon svn in the next hour  
or two.  It has also been merged over to the 1.6 branch and will  
appear in the next point release.

chris

On Feb 5, 2009, at 8:13 AM, Dan Bolser wrote:

> I don't know if I'm doing something wrong, but $hsp->significance
> seems to be undef when the evalue is 0 (parsing blastxml) with the
> latest version of the parser. The value should of course be 0 and not
> undef.
>
> Does anyone else see this (is it a known problem)?
>
>
> Cheers,
> Dan.
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