[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 
Bioperl.

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/

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
>
>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real 
> users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PGP.sig
Type: application/pgp-signature
Size: 186 bytes
Desc: This is a digitally signed message part
Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20050304/4e50a2a5/PGP.bin


More information about the Bioperl-l mailing list