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

[Scott Cain]

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