[Bioperl-l] compatibility problem of SeqIO

[Gert Thijs]

Marc,
Not at all, set1.tfa contains only 5 sequences of 800bp. 

Gert


On Fri, 2004-01-09 at 10:25, Marc Logghe wrote:
> Hi Gert,
> Is set1.tfa a large file ? If so, it might be that on one machine Perl is not supporting large files while on the other it does.
> HTH,
> Marc
> 
> > -----Original Message-----
> > From: Gert Thijs [mailto:gert.thijs at esat.kuleuven.ac.be]
> > Sent: Friday, January 09, 2004 10:05 AM
> > To: Bioperl
> > Subject: [Bioperl-l] compatibility problem of SeqIO
> > 
> > 
> > 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 1.59.2.4 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
> > +  ESAT-SCD 
> > +  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/
> > + 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > 
-- 
+ Gert Thijs          
+ Postdoctoral Researcher
+  K.U.Leuven
+  ESAT-SCD 
+  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/
+