Hello Monks, I seek you great wisdom. I'm fighting with a regex. The code: 

 while(defined ($file = readdir(DIR))) {
    next if $file =~ /^\.\.?$/; 
    if ($file =~ /_s_/) {
      $file = "../human/chr".$c.".fa/$file";
      foreach $tool (@$tools) {
    print $file,"\n";              #  <------ line 1
     $tool =~ s/<infile>/$file/;   #  <------ line 2
     print $tool,"\n";             #  <------ line 3
      }
    }
  }

[download]
Line 1 prints what I want. Line 3 prints only the first occurance of $file, so I'm guessing that the regex is only being compiled once with the first $file it "sees". My question: How the heck do I get the substitution to work for each value of $file, not just the first? Thanks Monks.

In reply to Substitution operator troubles by sabkat

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