[Bioperl-l] compatibility problem of SeqIO

[Marc Logghe]

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
>