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

[Zayed Albertyn]

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.

Z
On Fri, 14 Nov 2003, Andreas Kahari wrote:

> On Fri, Nov 14, 2003 at 12:34:53PM +0200, Zayed Albertyn wrote:
> > Hi Andreas
> >
> > Adding the -c switch still doesnt work. I still get the same error
> > message. Input is the full path to the file e.g.
> >
> > /cip0/db/GENBANK/RELEASE137/gbest13.seq.gz  == $path/$file
>
> Does the file "/cip0/db/GENBANK/RELEASE137/gbest13.seq.gz"
> exist or was it uncompressed into
> "/cip0/db/GENBANK/RELEASE137/gbest13.seq" when you ran the
> program which didn't use '-c' with gunzip?
>
>
>
> Andreas
>
> --
> |)()(|      Andreas Kähäri                                |{}{}|
> |()()|      EMBL, European Bioinformatics Institute       |}{}{|
> |)()(|      Wellcome Trust Genome Campus, Hinxton         |{}{}|
> |()()|      Cambridge, CB10 1SD                           |}{}{|
> |)()(|      United Kingdom                                |{}{}|
>

-----------------------------------------------
From: Zayed Albertyn
Electric Genetics PTY Ltd
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