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

[Zayed Albertyn]

Thanks alot guys. Could you please include that in further editions of
the HowTo?

You'll are doing a great job!

Zayed

On Fri, 14 Nov 2003, Andreas Kahari wrote:

> 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                                |(==)|
>

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From: Zayed Albertyn
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