Re^2: capture STDOUT without printing to screen

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

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Re^3: capture STDOUT without printing to screen by hmerrill (Friar) on Dec 07, 2004 at 12:47 UTC
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` [download] 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 [download] Anyway, hope that helps.	[reply] [d/l] [select]

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Re^3: capture STDOUT without printing to screen
by hmerrill (Friar) on Dec 07, 2004 at 12:47 UTC

   perldoc -q STDERR
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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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