[Bioperl-l] BLAT psl file to GTF

[Jamie Estill]

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

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
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