Substitution operator troubles

[sabkat]

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
      }
    }
  }

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.

[chromatic]

You're changing the array elements in-place. Once you've substituted away <infile>, it's gone for good. You could instead work on copies of the array elements:

foreach my $tool (@$tools)
{
    my $edit_tool =  $tool;
    $edit_tool    =~ s/<infile>/$file/ or next;
}

[cbro]

As far as I can tell you are only missing the global flag. That is:


$tool =~ s/<infile>/$file/;

Should be:


$tool =~ s/<infile>/$file/g;