[Bioperl-l] compatibility problem of SeqIO
gert.thijs at esat.kuleuven.ac.be
Fri Jan 9 04:05:29 EST 2004
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 220.127.116.11 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:
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
This is perl, v5.8.0 built for i386-linux-thread-multi
+ Gert Thijs
+ Postdoctoral Researcher
+ Kasteelpark Arenberg 10
+ B-3001 Leuven-Heverlee
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+ email: gert.thijs at esat.kuleuven.ac.be
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