[Bioperl-l] SeqFeature::Generic 'frame' method

[Ewan Birney]

On Mon, 26 Feb 2001, Jason Stajich wrote:

> That does seem safer.  I can easily transform from 1,2,3 to 0,1,2
> so frame +1 in blast will be equivalent to frame 0 in GFF. But what about
> cases where we don't have a frame, is Frame 0 technically correct there?

In cases where we don't have a frame it should be

   undef in perl and

   . in GFF.


> 
> Strand information for a HSP currently comes from direction
> of start/end points on the query seq.  Is it concievable that they
> wouldn't match?  i.e. will a match in -3 frame always correspond to a
> match on rev strand of query....  This might be a dilhema...  I already
> checked in code which breaks because of invalid frames, I will fix so it
> is at least transformed to valid number space of gff.  Strand will get
> ignored for now.
> 
> -Jason
> 
> On Mon, 26 Feb 2001, Hilmar Lapp wrote:
> 
> > Jason Stajich wrote:
> > > 
> > > Currently we only support frames of 0,1,2 as part of gff support I'm sure.
> > > However, as I try and map a TBLASTN HSP to a SeqFeature, frames
> > > can be -3,-2,-1,0,1,2,3.  Does anyone see problems with extending the
> > > supported values in the frame method to handle those above.  Does this
> > > break GFF standards somehow?  I can imagine someone parsing a blast
> > > report and writing the HSPs out as GFF features so it is quite likely that
> > > the two cases shall meet.
> > > 
> > 
> > Hmm. As long as there's a clear context of an HSP being the result of
> > parsing a Blast report there's no problem with extending the set of
> > allowed values. However, as soon as this context gets lost, like you
> > said (and going through GFF is not the only way to lose that), there's
> > a problem, because then frame 1 and frame 1 no longer mean the same
> > thing. Bad.
> > 
> > Can we map TBLASTN frame to the definitions we have set forth in
> > SeqFeatureI? E.g. TBLASTN parsed frame -3 would become SeqFeatureI
> > strand -1, frame 2. TBLASTN parsed frame 1 would be mapped to strand
> > 1, frame 0, and so forth. This would keep both the definitions and the
> > TBLASTN information.
> > 
> > The only remaining problem is TBLASTN frame 0. What does it mean? If
> > it's no frame, then it's equivalent to SeqFeatureI frame 0.
> > 
> > What do you think?
> > 
> > 	Hilmar
> > -- 
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp@gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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