for (my $annoIndex = 0; $annoIndex <= $#gbList; $annoIndex++) { my $currGB = $gbList[$annoIndex]; $startmark = 0; print "Current GB is $currGB\n"; for (my $lineIndex = 0; $lineIndex <= $#arraybl; $lineIndex++){ print "Line index is: $lineIndex\n"; my $lineinfile = $arraybl[$lineIndex]; print "line is: $lineinfile\n"; if (index($lineinfile, $currGB) != -1 || $lineinfile =~ m/$currGB/){ $startmark = $lineIndex+1; my @chunk = GetEntryLines($startmark); print "$currGB has been matched!\n"; #print "Chunk Length is $#chunk\n"; #-----------get rbcL & stuff------------ last; } else { next; } } }