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

[Brian Osborne]

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
> 
> 
> 
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