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use strict;
use warnings;
...
    s/,/;/g;
    print;
}

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$ perl test.pl 5378_scan.v >data.txt
$ cat data.txt
CK; n3065gat; n3066gat; n3067gat; n3068gat; n3069gat; n3070gat;n3100ga
+t; test_si; test_se;
n3104gat; n3105gat; n3106gat; n3107gat; n3108gat; n3109gat; n3110gat;