[Bioperl-l] compatibility problem of SeqIO

Gert Thijs 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 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

+ Gert Thijs          
+ Postdoctoral Researcher
+  K.U.Leuven
+  Kasteelpark Arenberg 10 
+  B-3001 Leuven-Heverlee  
+  Belgium  
+ Tel  : +32 16 327928 
+ Fax  : +32 16 321970
+ email: gert.thijs at esat.kuleuven.ac.be 
+  http://www.esat.kuleuven.ac.be/~thijs
+  http://www.esat.kuleuven.ac.be/~dna/BioI/

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