[Bioperl-l] Re: Determining strand orientation from bl2seq report

[Jason Stajich]

Patches accepted if you don't have an account (yet).  Submit a bug and a
patch for it at http://bugzilla.bioperl.org/


-jason

On Sat, 25 Jan 2003, Boris Lenhard wrote:

>
>
> > Dave - a little bit of detective work.  This stems from the fact that
> > bl2seq reports don't include information about which blast program was
> > used (blastn, blastp, etc) and that determines whether or not we set
> > stranded information or set it to 0 (for proteins).  Surprised this was
> > not caught before, I've added tests and testfiles to make sure this
> > doesn't happen again.
> >
> > I've committed changes to CVS allow you to specify the program used and
> > added tests for blastn bl2seq reports.  You can see how it works by
> > looking at t/BPbl2seq.t .
> >
> > Basically when you initialize a BPbl2seq object you add in the flag
> >
> > -report_type => 'blastn'
> >
>
> After this, one should perhaps also change the in
> Bio::Tools::Run::StandAloneBlast _runblast (line 650) to pass the
> object's p (program) parameter as -report_type to the
> Bio::Tools::BPbl2seq it calls. It is a god occasion for me to ask for a
> full cvs account, I guess :)
>
> In principle, a bl2seq report contains enough info to deduce indirectly
> which BLAST program produced it - from Strand or Frame lines (currently
> not used by the parser),  and  the end-start/hsp_length  ratio (3 or 1),
> so using that info instead of explicitly passing around the report type
> might be cleaner as a long-term solution.
>
> Boris
>
>
>
>

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