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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: Converting blast+ output to gff (with gaps)
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 2nd January 2013 22:26:55 UTC (over 3 years ago)
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  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 
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 
>> # 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 <[email protected]> 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
>>> [email protected]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> [email protected]
>> 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
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 
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