in reply to Re^5: System call doesn't recognise '>'
in thread System call doesn't recognise '>'

For this code:
my @array = ($command, $arg1, $arg2, $arg3);
system (@array);

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It runs perfectly and returns the output to StandardOUT

Clover: Cis-eLement OVERrepresentation
Compiled on Jul 18 2006

Getting raw scores...
Reading background sequences...
Analyzing background sequences...
Getting motif locations...
Sequence file: D:\advanced_programming\test.fa (3 sequences, 16050 bp,
+ 55.6% C+G)
Motif file: D:\advanced_programming\motif.dat (2 motifs)


*** Over- and Under-represented Motifs:

Motif  Raw score  P-value from randomizing
                  background

*** Motif Instances with Score >= 6:

Motif  Location     Strand  Sequence  Score

Background sequence files:
  D:\advanced_programming\background.fa (2 sequences, 284279 bp, 37.3%
+ C+G)
Randomizations:         1000
P-value threshold:      0.01
Motif score threshold:  6
Randomize nucleotides   OFF
Randomize dinucleotides OFF
Randomize motifs        OFF
Lowercase filtering     OFF
Pseudocount:            0.375
Random seed:            1

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This on the other hand: 

my @array = ($command, "$arg1 $arg2 $arg3");
system (@array);

[download]

Returns: 

Clover: Cis-eLement OVERrepresentation
Compiled on Jul 18 2006

Error: motif and sequence files required

Usage summary: clover [options] mymotifs myseqs.fa [BGfiles]

[download]

Replies are listed 'Best First'.
Re^7: System call doesn't recognise '>'
by cdarke (Prior) on Dec 10, 2008 at 16:08 UTC
    Use this:
    my $status = system ("$command $arg1 $arg2 $arg3 > $outfile");
if ($status) {
    print STDERR "Error: ", $status >> 8, "\n";
}

    [download]
[reply]
[d/l]
      That results in:

      Can't spawn "cmd.exe": No such file or directory at D:\advanced_progra
+mming\test_syscall.pl line 13.
Error: 255

      [download]
[reply]
[d/l]
Re^7: System call doesn't recognise '>'
by Bloodnok (Vicar) on Dec 10, 2008 at 16:21 UTC
    Ahh, methinx the mists begin to clear a little more (& not before time, I hear you say;-) ... '>' is an argument to the shell, not $command, thus if you need the output redirected in the manner you require, you'll have to use system "@array > $outfile" form - assuming @array contains $command.

    Alternatively you could use perl to perform the redirection by using open e.g. 

    open CMD, "@array > $outfile" or die "open() failed - $!";

    [download]
    In both cases, auto-stringifying the array.

    A user level that continues to overstate my experience :-))

[reply]
[d/l]
[select]
      my @array = ($command, $arg1, $arg2, $arg3);
system "@array > $outfile";

      [download]

      Results in: 

      Can't spawn "cmd.exe": No such file or directory at D:\advanced_progra
+mming\test_syscall.pl line 11.

and

my @array = ($command, $arg1, $arg2, $arg3);
open CMD, "@array > $outfile" or die "open() failed - $!";

      [download]

      gave: 

      Name "main::CMD" used only once: possible typo at D:\advanced_programm
+ing\test_syscall.pl line 17.
open() failed - Invalid argument at D:\advanced_programming\test_sysca
+ll.pl line 17.

      [download]
[reply]
[d/l]
[select]
Re^7: System call doesn't recognise '>'
by Corion (Patriarch) on Dec 10, 2008 at 16:18 UTC

    This code is not what was suggested:

    my @array = ($command, "$arg1 $arg2 $arg3");
system (@array);

    [download]

    What was suggested to you was:

    my @array = ($command, "$arg1 $arg2 $arg3");

system("@array");

# or, more verbose:

my $cmd = join " ", @array;
system ($cmd) == 0
    or die "Couldn't launch [$cmd]: $!/$?";

    [download]
[reply]
[d/l]
[select]
      Both ways you describe work perfectly, but do not redirect the output.
[reply]

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