This isn't very elegant, but you could scatter print statements through the suspect areas to see what is being executed and in what order and what your variable values are. 
$tesing = 1;
   .
   .
print "At second 'if' in do-loop, \$target_name is $target_name" if ($
+testing);
   .
   .

[download]
(untested)
Or something similar.

Theo

In reply to Re: Why is it matching?? by Theo
in thread Why is it matching?? by bioinformatics

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