[Bioperl-l] Re: [Gmod-gbrowse] Parser

Jason Stajich jason.stajich at duke.edu
Fri Mar 4 11:53:39 EST 2005

Bio::SearchIO::psl will pretty much do this for you.

There is a search2table script which may work out of the box or you may 
have to tweak a little to get the right fields to the right place.  It 
is in scripts/utilities/search2gff.pl.  There had been some off-by-one 
errors a while ago with the SearchIO psl parser, I *think* that is 
fixed now.

I don't know that anyone has contributed a RepeatMasker parser to 

Jason Stajich
jason.stajich at duke.edu

On Mar 4, 2005, at 12:45 PM, Thiago Motta Venancio wrote:

> Hi folks.
> Anyone here knows where can i find parsers that build GFF?
> I have one parser for RepeatMasker output and one for Blast output.
> I need a parser that converts PSL (Blat) output to GFF.
> Thanks in advance.
> Thiago
> -- 
> Thiago Motta Venancio - PhD student in Bioinformatics
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