[Bioperl-l] PullHSP bug

Sendu Bala bix at sendu.me.uk
Wed Dec 3 06:38:30 EST 2008

Chris Fields wrote:
> The short and easy fix is either having get_nse() or blast_pull fall 
> back to '', but both are technically wrong as there isn't a true ID.  
> Ideas?  Maybe a fallback 'unknown' ID (which seems to be used as a ).

I'd say for now at least the fix would be to alter get_nse() to fall 
back to ''. You don't want the work-around code duplicated in multiple 
places. Indeed, the normal blast parser should be altered to return 
undef as well.

Then if a more desirable solution is thought of in the future, there's 
just one place to implement it: in get_nse().

More information about the Bioperl-l mailing list