[Bioperl-l] Problem with Bio::SeqIO opening gzipped files

[Andreas Kahari]

On Fri, Nov 14, 2003 at 11:45:16AM +0200, Zayed Albertyn wrote:
[cut]
> my $seq_in = Bio::SeqIO::new(
>                                         '-file'  => "/bin/gunzip $path/$file |",
>                                         '-format' => 'genbank'
>                                     );
> }

You might find that you now have a lot of uncompressed files
lying around.

I believe you're missing the "-c" switch which makes gunzip send
its output to standard output.

    my $seq_in = Bio::SeqIO::new(
	'-file'   => "/bin/gunzip -c $path/$file|",
	'-format' => 'genbank'
    );



-- 
|()()|      Andreas Kähäri                                |(==)|
|)()(|      EMBL, European Bioinformatics Institute       |=)(=|
|()()|      Wellcome Trust Genome Campus, Hinxton         |(==)|
|)()(|      Cambridge, CB10 1SD                           |=)(=|
|()()|      United Kingdom                                |(==)|