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++;
}
}
}