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

[Jason Stajich]

with bp_search2gff  I included a cmdline options so you decide what is the reference (seqid column) and what is the target (9th column) since in some cases (BLASTX vs TBLASTN) you may want to be displaying one or the other as the reference. this is the -t option.

You can also have the -m option when you run which will build the grouping match term for a parent and then the sub-children will be HSPs that have that parent per Malcom's description of the parent child info.

Have you tried this with your output - it should work fine with regular vanilla text blast+ output or the -outfmt 6 option (tell bp_search2gff the format is blasttable)  or you can use -outfmt 5 and tell it you are using blastxml format.

 
Jason

On Jan 5, 2013, at 2:25 PM, Brian Osborne <bosborne11 at verizon.net> wrote:

> All,
> 
> The scripts/utilities/bp_search2gff.pl script works fine with blastn (BLAST+), no surprise there, and since it uses Bio::Tools::GFF it can produce GFF3.
> 
> Brian O.
> 
> 
> On Jan 2, 2013, at 5:53 PM, Brian Osborne <bosborne11 at verizon.net> 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
>>>>>> 
>>>>>> 
>>>>>> 
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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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>> 
>> 
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org