in reply to Re^2: System call doesn't recognise '>'
in thread System call doesn't recognise '>'

What happens if you make the call read: system("$command $arg1 $arg2 > outfile") ?

Note that, on Windoze, the arguments for system are the same as for exec. However, exec isn't, or wasn't, fully supported on Windoze, I think you might have to use the single string form of the call, so in your case, something along the lines of... 

my @array = qq/$command $arg1 $arg2 > outfile/;
system "@array"; # Use perl to stringify the command argument list

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Just a thought...

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

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Re^4: System call doesn't recognise '>'
by Lauras (Initiate) on Dec 10, 2008 at 15:00 UTC 
    my @array = qq/$command $arg1 $arg2 $arg3 > $outfile/;
system "@array";

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    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");

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    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]

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      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);

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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]
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