[Bioperl-l] compatibility problem of SeqIO

Gert Thijs gert.thijs at esat.kuleuven.ac.be
Fri Jan 9 09:57:10 EST 2004


That is the weird part, I am working on the same directory (over NFS). 
So permissions should be the same.

I have been playing around with this and I just found that the problem 
is probably caused by the way the input arguments are given to the 
script in which I use this command. If just type the name of the file as 
an input argument the script (myScript.pl set1.tfa} works, but if I 
write something like
   fasta_files='set1.tfa set2.tfa set3.tfa set4.tfa'
   for id in ${fasta_files}
     myScript.pl ${id}
then it does not work.
I find this rather disturbing.


Jason Stajich wrote:
> 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.
> -jason

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