It should (I recall using it at one point). If it doesn't we should fix it
so it does.
How does MAKER deal with this? IIRC it uses (a modified) SearchIO-based
On Jan 2, 2013, at 3:32 PM, Scott Cain wrote:
> Hi Brian,
> I was going to suggest the same thing--though that script is fairly
> old, it's not as old as the blast2gff script in the GBrowse
> distribution (which probably should be retired). I believe it
> supports GFF3, though I don't have any sample data with which to test
> it to be sure. I also don't know if it supports BLAST+ input--I
> haven't kept up with SearchIO (on which search2gff.pl depends); will
> it accept it?
> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne
>> Here's one:
>> Another one:
>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>> # Author: Jason Stajich
>> # Description: Turn SearchIO parseable report(s) into a GFF report
>> =head1 NAME
>> bp_search2gff - Turn SearchIO parseable reports(s) into a GFF report
>> Brian O.
>> On Jan 2, 2013, at 2:44 PM, Jim Hu <[email protected]> wrote:
>>> I assume this has already been done many times, but I can't seem to
find it on bioperl.org or via google.
>>> I'm looking for a script that will take one of the blast+ outformats
that includes the positions of gaps and mismatches, and create gff with
>>> Jim Hu
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> Bioperl-l mailing list
>>> [email protected]
>> Bioperl-l mailing list
>> [email protected]
> Scott Cain, Ph. D. scott at scottcain
> GMOD Coordinator (http://gmod.org/)
> Ontario Institute for Cancer Research
> Bioperl-l mailing list
> [email protected]