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read.txt
>s1
...
34 23 43 45 34 43 45 7 45 43 12 34 32 56 43
>s3
34 23 43 45 34 43 45 7 45 43 12 34 32 56 43

#!/usr/bin/perl
open(FH1,"read.txt");
...
print (join(' ',@num[@keep]),"\n");
}