[Bioperl-l] BLAT psl file to GTF

Amin Momin aminmom at hotmail.com
Fri Jul 22 16:16:58 UTC 2011

Thanks very much Jamie and Chris, Some of these scripts (DAWG PAWS) and bioperl modules will make my future work much quicker.


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 ..

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 commandcnv_blat2gff.pl --help 
will list the basic commands, andcnv_blat2gff.pl --manwill 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 athttp://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.


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


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James C. Estill
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