My guess is that your info is actually sent to STDERR. Try redirecting that to /dev/null in the command line. (nul on PC)

If you are running a *NIX, you may be able to do this:

my @lines_of_output = `sh /path/to/binary 2>&1`;
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You may not even need the 'sh' if your default shell supports the same redirection syntax. The '2>&1' tells the shell (which will execute your binary) to redirect all output on STDERR to STDOUT. STDOUT stuff will be left alone.

So, unless your external program is doing something odd like opening /dev/console or /dev/tty or something, the above should get you exactly what you'd otherwise see on the screen.

---

radiantmatrix
require General::Disclaimer;
Perl is

---

Hi Jared

My bet is that the program isn't writing to standard out else it wouldn't be printing to the screen when you run "myprog > somefile". It is more likely printing to STDERR.

Jason L. Froebe

update: I see Bart can type faster than I can :-)

It's also possible, although highly unlikely, that it's opening /dev/tty and writing to that rather than either of STD{OUT,ERR} (Presuming of course an *NIX system). In that case you'd have to use something like Expect or IPC::Run.

  my @output_lines_array = `/path/to/your_executable`;
  foreach my $line (@output_lines_array) {
     if (/^No. of sequences \(letters\): ([\d,])\s/) {
        print "No. of sequences = $1\n";
     }
  }
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I am using Mac OS X so it is unix. Here's my full code.

#!/usr/bin/perl -w
if (@ARGV==0) { 
   die "Usage: countseq.pl <dbname>\n";
}
my $prog = "/usr/ncbi/blast2/xdformat -n -i $ARGV[0]";
my $strOutput;
my @output = `$prog`;
foreach my $line (@output) {
   if (/^No. of sequences \(letters\): ([\d,])\s/) {
      $strOutput = $1;
   }
}
die "No output gathered \n" unless defined($strOutput);
print $strOutput;
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So from the shell here's what I get.

myshell$ ./countseq.pl human
Version
Release date:
Creation date: 2:17:09 AM EST Nov 19, 2004
Modified date: 2:17:09 AM EST Nov 19, 2004
Type: Nucleotide
Alphabet: NCBI2na(1)
No. of sequences (letters): 37,316 (33,115,935)
Longest sequence: 1542
Edit Alphabet: WUStLna(1)
Max. edits: 41
Total edits: 2693
37316
myshell$


I just want to see the number on the bottom (37316) Any thoughts? Any idea on how to determine if xdformat is printing to anything other than STDOUT?
Thanks, Jared

As 'jfroebe' said below, xpdformat is probably also writing to STDERR (which is *NOT* captured by backticks). Read about STDERR by doing

   perldoc -q STDERR
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at a command prompt. The perldoc '-q' says to search the perldoc documentation for string "STDERR". Here's a snippet from that:

Found in C:\Perl\lib\pod\perlfaq8.pod
  How can I capture STDERR from an external command?
    There are three basic ways of running external commands:

        system $cmd;                # using system()
        $output = `$cmd`;           # using backticks (``)
        open (PIPE, "cmd |");       # using open()

    With system(), both STDOUT and STDERR will go the same place as th
+e
    script's STDOUT and STDERR, unless the system() command redirects 
+them.
    Backticks and open() read only the STDOUT of your command.

Here's another snippet:
-----------------------

    You can also use file-descriptor redirection to make STDERR a dupl
+icate
    of STDOUT:

        $output = `$cmd 2>&1`;
        open (PIPE, "cmd 2>&1 |");

And another snippet:
--------------------

    ...To capture a command's STDERR and STDOUT together:

        $output = `cmd 2>&1`;           # either with backticks
        $pid = open(PH, "cmd 2>&1 |");  # or with an open pipe
        while (<PH>) { }                #    plus a read
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Anyway, hope that helps.