in reply to Calling Java using system()

Hi!
As system takes an array as an argument, I would rewrite your command like this: 
chdir("c:/users/sophix/Desktop/prottest3/prottest3/");
my @external_command = (
"java", 
"-jar prottest-3.0.jar", 
"-i ".$name."\.aa",  
"-t ".$name."\.trees", 
"-o ".$name."\.out" , 
"-all","-verbose",
"-all-matrices", "-threads 3",
"-G", "-F", "-all-distributions", "-ncat 4");
my $out = system(@external_command);

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What exactly would you like to do with your java program?
cpan:://IPC::Run3 works on various operating systems and allows you to process standard output and error messages from your java program separately.
Note: added chdir() after reading comment by saberworks Best wishes

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Re^2: Calling Java using system()
by sophix (Sexton) on Jun 24, 2011 at 19:57 UTC
    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");
    
}

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[reply]
[d/l]

      sophix:

      It looks like you ignored saberworks' suggestion. Your java.exe is probably not in the directory you specified. First change directories, then execute the code. Something like (untested):

      chdir("/usrs/sophix/Desktop/prottest3/prottest3");
my @ctl = glob("*.aa");
my ($ctltrimmed, $ctlfile, $ctlfiletrimmed);
foreach my $ctlfile (@ctl) {
    if ($ctlfile =~ m/(\S+).aa$/) {
        $ctlfiletrimmed = $1;
    }    

    my $out = system("java -jar prottest-3.0.jar -i " 
                     . $ctltrimmed . "-t " . $ctltrimmed 
                     . "\.trees" . "-o " . $ctltrimmed 
                     . "\.out" . "-all -verbose -all-matrices "
                     . "-threads 3 -G -F -all-distributions -ncat 4");
}

      [download]

      ...roboticus

      When your only tool is a hammer, all problems look like your thumb.

[reply]
[d/l]

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