[Bioperl-l] BLAT psl file to GTF

[Jamie Estill]

I've never really needed to convert to GTF, but at one point bioperl
supported gtf as gff 2.5

http://doc.bioperl.org/releases/bioperl-1.5.1/Bio/FeatureIO/gff.html

So once blat data are in gff3, a conversion from gff3 to gtf would work like


my $inGFF = Bio::FeatureIO->new( '-file' => "$inFile",
 '-format' => 'GFF',
 '-version' => 3 );my $outGTF = Bio::FeatureIO->new( '-file' => ">$outFile",
 '-format' => 'GFF',
 '-version' => 2.5);
 while (my $feature = $inGFF->next_feature() ) {

 $outGTF->write_feature($feature);
 }


see discussion at

http://sunnyjoy.wikispaces.com/convert+GTF+to+gff3


On Fri, Jul 22, 2011 at 12:16 PM, Amin Momin <aminmom at hotmail.com> wrote:

>  Thanks very much Jamie and Chris, Some of these scripts (DAWG PAWS) and
> bioperl modules will make my future work much quicker.
>
> Amin
>
> ------------------------------
> Date: Fri, 22 Jul 2011 11:17:37 -0400
> Subject: Re: [Bioperl-l] BLAT psl file to GTF
> From: jamesestill at gmail.com
> To: cjfields at illinois.edu
> CC: aminmom at hotmail.com; bioperl-l at lists.open-bio.org
>
>
> I wrote a blat2gff converter that worked the last time I used it ..
>
>
> http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/trunk/scripts/cnv_blat2gff.pl?revision=994&content-type=text%2Fplain<http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/trunk/scripts/cnv_blat2gff.pl?revision=994&content-type=text/plain>
>
> It is a simple/fast converter with minimal dependencies. Let me know if you
> try it and it works or does not work for you.
>
> The command
> cnv_blat2gff.pl --help
> will list the basic commands, and
> cnv_blat2gff.pl --man
> will pull up the man page.
>
> This is part of a larger set of conversion/annotation programs
> http://dawgpaws.sourceforge.net/
> with the source repository of scripts available at
> http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/trunk/scripts/
>
> -- Jamie
>
> On Fri, Jul 22, 2011 at 10:56 AM, Chris Fields <cjfields at illinois.edu>wrote:
>
> Bio::SearchIO::pal is one way, though I recall a psl2gff script (maybe from
> Don Gilbert?) out there somewhere that might be more up-to-date and faster.
>
> chris
>
> On Jul 21, 2011, at 9:19 AM, Amin Momin wrote:
>
> >
> > Hi ,
> >    I have been trying to convert a .psl file from BLAT into a GTF file.
> Is there a bioperl module capable of performing this. Or any tool that can
> be used to perform similar conversion.
> >
> > Amin
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
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>
>
>
>
> --
> -----------------------------------------
> James C. Estill
> JamesEstill at gmail.com
> http://jestill.myweb.uga.edu
> -----------------------------------------
>



-- 
-----------------------------------------
James C. Estill
JamesEstill at gmail.com
http://jestill.myweb.uga.edu
-----------------------------------------