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#!/usr/bin/perl
use strict;
use warnings;
...
        ++$neutral_cnt;
    }
}

C:\Old_Data\perlp>perl t7.pl
aa D pos: pos reset
aa K pos: 1

C:\Old_Data\perlp>perl t9.pl test.fas

...
Number of acidic amino acids:14
Number of basic amino acids:18
Number of neutral amino acids:67