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

[Brian Osborne]

Scott and Chris,

I'll test it and see…

Brian O.


On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> 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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>>> 
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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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>