In your templating system, have the positions interpolate as a string instead of using a literal variable $mydata. If you can show us a (tiny) example script that does what you describe, we can likely point out better what you need to change.
Basically, I imagine your script being:
#!perl -w
use strict;
my $mydata = "[[0,170],[1,27],[2,3],[3,0],[4,0],[5,0],[6,0],[7,0],[8,0
+],[9,0],[10,0]]";
print <<'HTML';
<html>
<head>
<script src="jquery.js"></script>
<script>
var data=$mydata;
</script>
</head>
<body>
<h1>Hello</h1>
</body>
HTML
In that case, the easiest approach would be to change the interpolation to double quotes.
The best approach is to use a proper templating system like HTML::Template or Template::Toolkit.
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