Hi,

Rewriting did not work.

The program I am using is called ProtTest - it is a Java application. http://darwin.uvigo.es/software/prottest3/prottest3.html

I am able to run this program for a single file, but I have a huge number of files and I want to loop them processing one bye one

So this is the snippet I wrote: 

my @ctl = glob("/users/sophix/Desktop/prottest3/prottest3/*.aa");

my ($ctltrimmed, $ctlfile, $ctlfiletrimmed);

foreach my $ctlfile (@ctl) {

    if ($ctlfile =~ m/prottest3\/prottest3\/(\S+).aa$/) {$ctlfiletrimm
+ed = $1;}    

    my $out = system("/users/sophix/Desktop/prottest3/prottest3/java.e
+xe -jar prottest-3.0.jar -i " . $ctltrimmed . "-t " . $ctltrimmed . "
+\.trees" . "-o " . $ctltrimmed . "\.out" . "-all -verbose -all-matric
+es -threads 3 -G -F -all-distributions -ncat 4");
    
}

[download]

In reply to Re^2: Calling Java using system() by sophix
in thread Calling Java using system() by sophix

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