Hi

I don't think I quite understand what you are aiming to do. Perhaps if you posted the desired output to go with the input data, it would be clearer.

But here are some notes on your code:

• use strict; use warnings; and probably use diagnostics;
• Indent your code to show what is in the while loop.
• You seem to be opening and closing the output file within the while loop - this means you'll only have the most recent line from the input file in the output file.
• You should check the return code from opening the output file as well as the input file.
• substr($_, 7, $x) where $x = length($_) - 7 seems to be taking the rest of the line after character 7. You can do that with substr($_, 7)
• For me, your code outputs to test_se, not n3070gat.

Taking a guess at what you want to do, try this for starters:

use strict;
use warnings;
use diagnostics;

while (<>) {
    s/^\s*input\s*//;
    s/^\s*output\s*//;
    s/,/;/g;
    print;
}
[download]

This simply strips 'input' and 'output' from the starts of the lines (with variable amounts of white space) and turns ',' into ';'. I have done it using <> so that it will act as a filter. You specify the input and output files on the command line e.g.

$ 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;
[download]

If you decide to open the files within the script, look up using the 3-argument form of open, lexical file handles and checking the return value of open.

Come back and say if this helps, and any other questions you have.

Regards, F.V.S.