[Bioperl-l] compatibility problem of SeqIO

Jason Stajich jason at cgt.duhs.duke.edu
Fri Jan 9 08:35:11 EST 2004

if you add this in your script it can give some information about whether
or not you can read the file.

if( -r $seqFile ) {
 print "I can read $seqFile\n";
} else {
 print "I cannot read $seqFile\n";

you can also try
open($fh, $seqFile) || die( "$seqFile: $!\n");

You should check file permissions, that you are running in the proper
directory, etc.

On Fri, 9 Jan 2004, Gert Thijs wrote:

> Dear,
> I have a script that behaves differently on two different linux PCs. The
> problem is caused by the following code, which seems rather trivial:
>   my $seqFile = 'set1.tfa';
>   my $seqio = new Bio::SeqIO( -file => "<$seqFile",
>                               -format => 'fasta');
>                                                                                                                                               On the first machine it works without any problem, but on the other one I get an error saying 'Could not open <set1.tfa:  No such file or directory', while the fasta file is present.
> Has anyone an idea what could cause this different behavior?
> I have added the system information below and to me it seems that both
> configurations are more or less the same.
> In both cases I use the same version of bioperl.
> Here is the header of SeqIO.pm, which is the same on both machines.
> # $Id: SeqIO.pm,v 2003/09/14 19:16:53 jason Exp $
> The configuration of the first machine is:
>   [thijs at sista-08 thijs]$ cat /proc/version
>   Linux version 2.4.22-10mdk (nplanel at no.mandrakesoft.com) (gcc version
> 3.3.1 (Mandrake Linux 9.2 3.3.1-2mdk)) #1 Thu Sep 18  12:30:58 CEST 2003
>   [thijs at sista-08 thijs]$ perl -v
>   This is perl, v5.8.1 built for i386-linux-thread-multi
> The configuration of the second one is:
>   val3|thijs>cat /proc/version
>   Linux version 2.4.20-24.9smp (bhcompile at porky.devel.redhat.com) (gcc
> version 3.2.2 20030222 (Red Hat Linux 3.2.2-5)) #1 SMP Mon Dec 1
> 11:25:17 EST 2003
>   val3|thijs>perl -v
>   This is perl, v5.8.0 built for i386-linux-thread-multi

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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