[Bioperl-l] Hspwriter and fasta

[Jason Stajich]

This has to do with HSPTableWriter expecting fields that are specific to
the BlastHSP not in the HSPI interface -- something that no one has gotten
around to fixing.  So it is probably not going to work until someone goes
in there and fixes the HSP/Result/HitTable writer -- mind you the
HTML/TextResult writers do work by only expecting interface.

-jason

On Fri, 27 Sep 2002, Vilanova,David,LAUSANNE,NRC/BS wrote:

> Hello,
> I'm just trying to parse and write a Fasta report using HSPtableWriter but
> this is what I'm getting :
>  0               0       0       0       0.0e+00 0       0       0.00
>
>
> Here below is an extract of the script. I think it has something to do with
> HSPtableWriter
>
> my $writer = new Bio::SearchIO::Writer::HSPTableWriter;
> my $out = Bio::SearchIO->new( -writer => $writer,
> 							  -file   => ">out"
> );
> my $searchio = new Bio::SearchIO(-file=>"report.FASTA",
>
> -format=>'fasta');
>
> my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(
> 								-columns =>
> [qw(
>
> query_name
>                                                   query_length
>
> hit_name
>
> hit_length
>
> rank
>
> frac_identical_query
>
> expect
>
> )]
>
> );
>
>
> 	while ( my $result = $searchio->next_result() )
> 			{
> 	       $out->write_result($result);
>
> 		    }
>
> David
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu