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use v5.16;
use strict;
...
    if   ( $_ % 2 == 0 ) { print qq[-x$count=$pts[$_]] }
    else                 { print qq[-y$count=$pts[$_]]; $count++ }
}

prBoundaryString='( (0.01 0.02) (0.0 1328.23) (0.01 0.02) (0.04 0.53) 
+(0.03 44.23)
   (0.0 1328.23) (0.04 0.53)
...
-y5=1328.23
-x6=0.04
-y6=0.53