Read your index file into a hash:
open my $idx, '<', 'index.file' or die "Can't open 'index.file' for re
+ading: $!";
my %index;
while (<$idx>){
chomp;
$index{$_} = 1;
}
And then go through your data file, and replace as needed while copying to a temporary file:
while (<$in>) {
if ($index{$.}){
s/foo/bar/g;
}
print $tmp $_;
}
When you're done, override the data file with the temporary file.
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