I am using AMPHORA2
for phylotyping. And I am stuck at the third script because the counter does not increase at all because it possibly cannot find a match.
my $count = 0;
open (IN, "$marker.aln") ||die "cant open $marker.aln";
while (<IN>) {
$count++ if /REF-/;
}
close IN;
$count
is always 0. and this counter is used for division purpose later on. Therefore, the run is stuck. Anyone encountered the same problem? And/or solved this issue?