[Bioperl-l] search2gff

Jason Stajich jason at cgt.duhs.duke.edu
Sun Jul 4 13:30:56 EDT 2004

On Fri, 2 Jul 2004, Neil Saunders wrote:

> I have a couple of queries regarding the search2gff script.
> 1) I'm using the latest CVS (1.8) which states "search2gff does the
> right thing now - now strand is done right properly".  Am I right in
> thinking that now target start is always less than target end?

> 2) Should search2gff work with any BLAST flavour?
> I ask because I'm running it on tblastx files.  Without the -m switch
> it seems to run fine, but if I add -m, I get thrown exceptions looking
> like e.g. :
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Undefined sub-sequence (2827710,2827711). Valid range = 2827710 -
> 2827889
> The undefined subsequence start/ends always differ by 1.

Can you send the whole stack trace and/or better an example blast file.  I
guess ideally this should be submitted as a bug.  I don't see any calls to
matches in the code so I am not sure why this is getting triggered.
I changed the script again to be a little simpler so might pull from
latest CVS again.

> thanks,
> Neil

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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