use stricts;
use warnings;

my $total_entry_non_barrel='';
my $aligns_non_barrel='';
my @split_aligns_non_barrel=();
my $separate_hit_non_barrel='';
my @split_hit_non_barrel=();
my $hit_line_non_barrel='';
my $hit_name_non_barrel='';
my $protein_non_barrel='';
my $stat_line_non_barrel='';
my @split_stats_non_barrel=();
my $score_non_barrel='';
my $conditional_evalue_non_barrel='';
my $env_start_non_barrel='';
my $env_end_non_barrel='';
my $i=0;
my $k=0;

$/="//\n";
while(<>)
{
	$total_entry_non_barrel=$_;
	if($total_entry_non_barrel=~/^Query:\s+(.*?)\s\[L=(\d+)\]/m)
	{
		$protein_non_barrel=$1; 
	}

	if ($total_entry_non_barrel!~/No hits detected/)	
	{
		if($total_entry_non_barrel=~/Domain annotation for each model:(.*)Internal pipeline statistics summary:/s)
		{
			$aligns_non_barrel=$1; 
			@split_aligns_non_barrel=split(">> ", $aligns_non_barrel);

			for($i=0; $i<=$#split_aligns_non_barrel; $i++)
			{
				$separate_hit_non_barrel=$split_aligns_non_barrel[$i];
				@split_hit_non_barrel=split(/\n/, $separate_hit_non_barrel);
				$hit_line_non_barrel=$split_hit_non_barrel[0];
				if($hit_line_non_barrel=~/^(.*?)\s+/)
				{
					$hit_name_non_barrel=$1;
				}

				#keep score, c-Evalue, env-start, env-end for each hit
				for($k=3; $k<=$#split_hit_non_barrel; $k++)
				{
					$stat_line_non_barrel=$split_hit_non_barrel[$k];
					@split_stats_non_barrel=split(/\s+/, $stat_line_non_barrel);
					$score_non_barrel = $split_stats_non_barrel[3];
					$conditional_evalue_non_barrel = $split_stats_non_barrel[5];
					$env_start_non_barrel = $split_stats_non_barrel[13];
					$env_end_non_barrel = $split_stats_non_barrel[14];
				}

				if($hit_name_non_barrel=~/^PF\d+/)		#it is a PFAM-A hit, keep it if score >=TC
				{
					if($score_non_barrel>=$hash_pfamA_tc{$hit_name_non_barrel})
					{
						print $hit_name_non_barrel, "\t", $score_non_barrel, "\t", $conditional_evalue_non_barrel, "\t",$env_start_non_barrel , "\t", $env_end_non_barrel, "\n"; 
					}
				}

				elsif($hit_name_non_barrel=~/^PB\d+/)	#it is a PfamB hit, keep it if Evalue<=1e-6
				{
					if($conditional_evalue_non_barrel<=0.000001)
					{
						print $hit_name_non_barrel, "\t", $score_non_barrel, "\t", $conditional_evalue_non_barrel, "\t",$env_start_non_barrel , "\t", $env_end_non_barrel, "\n"; 
					}
				}
			}
		}
	}
	print "##\n";
}
$/="\n";

##</code><code>##

Use of uninitialized value $hit_line_non_barrel in pattern match (m//) at ttt.pl line 735

##</code><code>##

if($hit_line_non_barrel=~/^(.*?)\s+/)