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

[Jim Hu]

Thanks for the replies, but...

I can't tell what input formats for the blast results file are supported.  Format 11 and format 6 give no output and no feedback. Putting some diagnostic print statements in the code suggests that I'm not getting any result objects from Bio::SearchIO.

The script uses Bio::SearchIO, but does not seem to call the submodules for blast.  Documentation links on the wiki seem to be broken, at least on this page:

	http://www.bioperl.org/wiki/Module:Bio::SearchIO

Jim


On Jan 2, 2013, at 4:53 PM, Brian Osborne wrote:

> 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
>>>>> 
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> 
>>>> 
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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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 

=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054