in reply to Re^3: System call doesn't recognise '>'
in thread System call doesn't recognise '>'

my @array = qq/$command $arg1 $arg2 $arg3 > $outfile/;
system "@array";

[download]

Resulted in: Can't spawn "cmd.exe": No such file or directory at D:\advanced_programming\test_syscall.pl line 10.

On the other hand: 

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

[download]

system (@array);

Results in:

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^5: System call doesn't recognise '>'
by Bloodnok (Vicar) on Dec 10, 2008 at 15:05 UTC
    Does the command work without redirection when run by system?

    A user level that continues to overstate my experience :-))
[reply]
[d/l]
      For this code:
      my @array = ($command, $arg1, $arg2, $arg3);
system (@array);

      [download]

      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

      [download]

      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]
[reply]
[d/l]
[select]
        Use this:
        my $status = system ("$command $arg1 $arg2 $arg3 > $outfile");
if ($status) {
    print STDERR "Error: ", $status >> 8, "\n";
}

        [download]
[reply]
[d/l]
        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]

        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]

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