Fields, Christopher J | 2 Jan 23:26 2013

Re: Converting blast+ output to gff (with gaps)

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
>>> 
>>> 
>>> 
>>> _______________________________________________
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>>> Bioperl-l <at> lists.open-bio.org
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>> 
>> 
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> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
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Gmane