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

Jason Stajich jason.stajich at duke.edu
Fri Mar 4 16:06:35 EST 2005

You'll have to read-up on the SearchIO system for it to make any sense.

The HSPs are the "features" which are written back out with the 
Bio::Tools::GFF module.

Most of the work is already done in the search2gff.PLS script for you 
-- there is a lot of code in there to handle asking for query or hit 
strand (you can only output one or the other) and filtering.

The code is in bioperl scripts/utilities directory or you can pull it 
down here:

So you want to run it like this (argument order doesn't matter)
perl search2gff -o myout.gff -i myinput.psl -f psl

Jason Stajich
jason.stajich at duke.edu

On Mar 4, 2005, at 1:07 PM, Thiago Motta Venancio wrote:

> Dear Jason.
> Thanks for replying me.
> I saw the documentation of your package before writing to the list, 
> but i did not understand how to use it.
> Sorry about my low knowledge in Bioperl.
> Here is your code:
> use Bio::SearchIO;
>  my $parser = new Bio::SearchIO(-file   => 'file.psl',
>                                 -format => 'psl');
>  while( my $result = $parser->next_result ) {
>  }
> The question is where to specify the GFF format...
> Regards.
> Thiago
> -- 
> Thiago Motta Venancio - PhD student in Bioinformatics
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