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

[Andreas Kahari]

On Fri, Nov 14, 2003 at 12:52:25PM +0200, Zayed Albertyn wrote:
> The file does exist as
> 
> -rwxrwxrwx    1 dbases   sanbi    21510739 Sep 27 23:27 /cip0/db/GENBANK/RELEASE137/gbest13.seq.gz
> 
> I always supplied a gzipped file and printed it's name to check what files
> are being worked on.
> 
> I even added an  "if (-e "$path/$file") " to the loop and it still went in
> to try and open the file.
> 
> 
> But I cannot write to the directory it is in. So without the -c switch I
> wont be able to decompress it anyway unless I make a copy in my own
> directory. I have tried that with and without the -c switch. gunzip does
> the job but I cant get around that internal method error.
[cut]

I think this is where you let us know what version of bioperl
you're using and what system you're on.

Using fresh bioperl 1.2.3 installation on OpenBSD, I have no
problem reading genbank data off a gunzip pipe.

It would be useful to see a minimal, yet complete, program that
exhibits the behaviour you're mentioning.


Andreas

-- 
|[--]|      Andreas Kähäri                                |-}{-|
|-][-|      EMBL, European Bioinformatics Institute       |{--}|
|[--]|      Wellcome Trust Genome Campus, Hinxton         |-}{-|
|-][-|      Cambridge, CB10 1SD                           |{--}|
|[--]|      United Kingdom                                |-}{-|