use strict; { local $/ = 'output'; while () { chomp; # drop 'output' my (undef, $line) = split /input/; $line =~s/,/;/g; print "$line\n"; } } __DATA__ input CK, n3065gat, n3066gat, n3067gat, n3068gat, n3069gat, n3070gat,n3100gat, test_si, test_se; output n3104gat, n3105gat, n3106gat, n3107gat, n3108gat, n3109gat, n3110gat; input CK, n3065gat_2, n3066gat_2, n3067gat_2, n3068gat_2, n3069gat_2, n3070gat_2,n3100gat_2, test_si, test_se; output n3104gat_2, n3105gat_2, n3106gat_2, n3107gat_2, n3108gat_2, n3109gat_2, n3110gat_2; input CK, n3065gat_3, n3066gat_3, n3067gat_3, n3068gat_3, n3069gat_3, n3070gat_3,n3100gat_3, test_si, test_se; output n3104gat_3, n3105gat_3, n3106gat_3, n3107gat_3, n3108gat_3, n3109gat_3, n3110gat_3; input CK, n3065gat_4, n3066gat_4, n3067gat_4, n3068gat_4, n3069gat_4, n3070gat_4,n3100gat_4, test_si, test_se; output n3104gat_4, n3105gat_4, n3106gat_4, n3107gat_4, n3108gat_4, n3109gat_4, n3110gat_4;