[Bioperl-l] Converting blast+ output to gff (with gaps)

[Fields, Christopher J]

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 method... 

chris

On Jan 2, 2013, at 3:32 PM, Scott Cain <scott at scottcain.net> 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?
> 
> Scott
> 
> 
> On Wed, Jan 2, 2013 at 3:26 PM, Brian Osborne <bosborne11 at verizon.net> wrote:
>> Here's one:
>> 
>> https://github.com/GMOD/GBrowse/blob/master/contrib/blast2gff.pl
>> 
>> Another one:
>> 
>> ~/git/bioperl-live>head scripts/utilities/bp_search2gff.pl
>> #!perl
>> 
>> # Author:      Jason Stajich <jason-at-bioperl-dot-org>
>> # 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 <jimhu at tamu.edu> 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 appropriate subfeatures.
>>> 
>>> Thanks,
>>> 
>>> Jim
>>> =====================================
>>> Jim Hu
>>> Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l