Thanks for all the help!
Here is a simple coding question I suspect you may be able to help me with.
Here is a slice from my first subroutine.
In it, I am going to try to basically put the first line of each fasta sequence into a key, and the coding lines of the fastA sequences into the hash.

I am trying to use the /$search/gi code near the bottom in order to find how many times my search sequences are found amongst ALL the sequences.
AKA, if I search for the amino acid "R", it should come up 350 times. However, $hits is instead equal to 55.
Basically it stops searching once a line is classified as containing "R", and gives me the number of lines which satisfy the condition, rather than the amount of times the search sequence is found.


    while (my $line =<INPUT>) {
      if ($line =~m/^>/) {
    if ($seq) {
      $o{$header} = "$seq";
    }
    $count++;
    print "\n\n";
    print "$line";
    $header = "$line";
    $seq=();
      } else {
    chomp $line;
    print $line;
    $seq .= "$line";
    if ($line =~/$search/gi) {
      $hits++;
    }
      }
    }

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In reply to Re^2: FASTA riddle. by MaroonBalloon
in thread FASTA riddle. by MaroonBalloon

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