In the original you are searching for two strings in the same line but in the new version you are searching for one string in one line and the other string in the next line.

Also, you are using the high precedence || operator which means that the program will not die if open fails because you are testing the boolean state of the string 'sample.fa' or the string '>modsample.fa' which are always true.

You probably want something like this:

open IN,  '<', 'sample.fa'    or die "Could not open 'sample.fa' becau
+se: $!";
open OUT, '>', 'modsample.fa' or die "Could not open 'modsample.fa' be
+cause: $!";

my $previous;
while ( my $line = <IN> ) {
    if ( $previous && $line =~ /mamma/ && $line =~ /mia/ ) {
        print OUT $previous, $line;
        }
    else {
        print ".";
        }
    $previous = $line
    }

[download]

Thanks = looks like I had been really crosseyed with that. Good that I could borrow your eyes for a second. (Long time no scripting .. have to learn to pay more attention)

Once you've read a line from <IN>, it is "used up", and the next call to <IN> will return the line after it.

So when you do

while ($line = <IN>)
{$nextline=<IN>;
[download]

You're reading two lines, and so overall $nextline will only contain every second line in the file (all even-numbered lines if you start counting from 1).

So if all the matches are on odd-numbered lines, you won't see anything ini the output.

Try something like this instead:

my $previous = '';
while ($line = <IN>) {
     if ($line =~ /mamma/ && $line =~ /mia/) {
          print OUT $previous;
          print OUT $line;
     } else {
          print ".";
     }
} continue {
    $previous = $line;
}
[download]

That way $line sees all the lines in the input file, and you still have the previous line available inside the loop.

Actually it is my intent to read and find matches only in every second line. The input line as a format like this. >headline1 linethatactuallycontainsthematchesiminterestedin1 >headline2 linethatactuallycontainsthematchesiminterestedin2 But thanks for mentioning. It might have been a great ocersight. Like the oversight I actually made (did not replace both lines with nextline)

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