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

Jason Stajich jason@chg.mc.duke.edu
Mon, 26 Feb 2001 17:35:53 -0500 (EST)

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.

Jason Stajich
Center for Human Genetics
Duke University Medical Center