[Bioperl-l] Hspwriter and fasta

[Aaron J Mackey]

Can you send me your report.FASTA, perhaps privately?  I'm working on
something of an overhaul of the fasta parser, and perhaps you've hit a
snag in the current logic ...

-Aaron

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
>
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-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu