in reply to Calling a subroutine within a conditional

"TRUE" is a string. You should use $continue_tag eq "TRUE" to compare strings.
Boris

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Re^2: Calling a subroutine within a conditional
by Freezer (Sexton) on Sep 03, 2012 at 12:39 UTC
    I fixed that, but still get: 
    
main::look_through_file() called too early to check prototype at recei
+ve_annotations_B.pl line 47.
main::create_output() called too early to check prototype at receive_a
+nnotations_B.pl line 48.

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    :(
[reply]
[d/l]
      Where do you define the subroutines? If they are in the same package, move them above the main part of the code; that's better style anyway.
[reply]

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