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Gmane
From: Jason Stajich <jason.stajich <at> gmail.com>
Subject: Re: Converting blast+ output to gff (with gaps)
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 7th January 2013 09:35:23 UTC (over 3 years ago)
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  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  wrote:
> 
>> Scott and Chris,
>> 
>> I'll test it and seeā€¦
>> 
>> Brian O.
>> 
>> 
>> On Jan 2, 2013, at 5:26 PM, "Fields, Christopher J"
 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  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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> 
> 
> _______________________________________________
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Jason Stajich
[email protected]
[email protected]
 
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