You don't even have to do the indentation manually, Perl::Tidy will do it for you: $ perltidy your-script.pl (output goes to your-script.pl.tdy). Also, you can get some useful information from Perl::Critic:

$ perlcritic your-script.pl
Loop iterator is not lexical at line 13, column 1.  See page 108 of PB
+P.  (Severity: 5)
Bareword file handle opened at line 15, column 1.  See pages 202,204 o
+f PBP.  (Severity: 5)
Two-argument "open" used at line 15, column 1.  See page 207 of PBP.  
+(Severity: 5)
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Update: As for your concrete problem, can you supply some (scrambled) input data?