in reply to Re^2: quoting issue with system command
in thread quoting issue with system command

Put the exe name in quotes, too: 
"D:\Program Files\foo.exe" arg1 arg2 "file_name with spaces.txt"

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The logic of system's argument processing is supposed to make sense on Unix, with underlying OS primitives that work in the same way. But it's a mess on Windows, where the documented meaning is implemented to some degree. Point is, it takes different code paths depending on the form, with different behavior. It's been a while since I looked at it. But if it calls the CMD.exe shell with the whole thing as a string, it behaves the same way as on the command line, as I showed. If it tries to call CreateProcess directly, the exe file name is a separate argument to that.

I suppose I should refresh my knowledge before writing anything that makes use of that feature myself.

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Re^4: quoting issue with system command
by lomSpace (Scribe) on May 13, 2009 at 17:46 UTC
    So something like this:

    my $command = “c:\\blast\bin\\blastall.exe" -p blastn -d "$hu_seq $hd_seq" -i "$contig" -o $alignment”;
    print "$command\n";
    system($command);
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      Better: 
      my @command = ("c:\\blast\bin\\blastall.exe",
   -p => 'blastn',
   -d => "$hu_seq $hd_seq",
   -i => $contig,
   -o => $alignment,
);
system(@command);

      [download]

      Note: You've got a problem if -d expects space-separated paths if the paths have spaces in them.

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[d/l]
[select]
      You are missing putting delimiters around the whole thing.
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Re^4: quoting issue with system command
by lomSpace (Scribe) on May 13, 2009 at 18:04 UTC
    Oh, I am using it on Windows. My path is :

    $hu_seq is 'I:\13414 Ccl9 (88)\sequencing\13414_hu.fa'
    $hd_seq is 'I:\13414 Ccl9 (88)\sequencing\13414_hd.fa'

    This is what I am passing to the system command.
    my @command2 =('c:\\blast\\bin\\blastall.exe','-p', 'blastn','-d',"$hu_seq $hd_seq",'-i', $contig,'-o', $alignment);

    I am getting the following error message:

    NULL_Caption ERROR: Could not open i:\13414
    NULL_Caption ERROR: Arguments must start with '-' (the offending argument #7 was: 'Ccl9')

    I think that this is why I am unable to build the blastsearchable db.
    How do I get around those space in path to the variable?
    Thanks!
    LomSpace
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