Still works fine for me even with XML input:

$ cat base.xml
<?xml version="1.0" encoding="UTF-8"?>
<root>
    <foo>bar</foo>
</root>
$ perl 11109932.pl < base.xml
This is what line looks like <?xml version="1.0" encoding="UTF-8"?>
 
This is what line looks like <root>
 



.ELEPHANTS
This is what line looks like     <foo>bar</foo>
 



.ELEPHANTS
This is what line looks like </root>
 



.ELEPHANTS
$
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Your steadfast reluctance to provide an SSCCE is doing you no favours.