Re^2: Calling Java using system()

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]

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Re^3: Calling Java using system() by roboticus (Chancellor) on Jun 24, 2011 at 20:15 UTC
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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Re^3: Calling Java using system()
by roboticus (Chancellor) on Jun 24, 2011 at 20:15 UTC

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]