adding a missing file caused by git

bin/lincRNA_classification.pl

@@ -0,0 +1,83 @@
+#!perl
+use strict;
+use warnings;
+
+#input format
+die "USAGE: lncRNA_file genecode_file OUT_file" unless @ARGV == 3;
+open IN1,"$ARGV[0]" || die "$!";
+open IN2,"$ARGV[1]" || die "$!";
+open OUT,"> $ARGV[2]" || die "$!";
+my %gene_data;
+my %gene_dir;
+#read genecode file and store the data
+while(<IN2>){
+	chomp;
+	my @data = split /\t/,$_;
+	if ($data[2] ne 'exon'){
+		next;
+	}
+	$data[8] =~ /gene_name\s\"(.*)\";\stranscript_type/;
+	my $gene_name = $1;
+	my @arr = [$data[3],$data[4]];
+	push(@{$gene_data{$gene_name}},@arr);
+	$gene_dir{$gene_name} = $data[6];
+}
+
+#read the lncRNA file per line and classify
+my @results;
+while(<IN1>){
+	chomp;
+	my $result;
+	my $smname;
+	my @data = split /\t/,$_;
+	#if ($data[8] !~ /transcript_id\s\"LINC/){        #remove not LINC
+	#	next;
+	#}
+	my @rna = split /;/,$data[8];
+	$rna[1] =~ /\"(.*)\"/;
+	my $linc = $1;
+	$rna[2] =~ /\"(\d+)\"/;
+	my $distance = $1;
+	$_ =~ /closet_gene "(.*)"/;
+	$smname = $1;
+	if ($distance > 1000){                             #c1
+		$result = $linc."\t"."Intergenic";
+		push(@results,$result);
+	}elsif($distance > 0){                             #c1 and c2      
+		if($gene_dir{$smname} eq $data[6]){
+			$result = $linc."\t"."Intergenic";
+			push(@results,$result);
+		}else{
+			$result = $linc."\t"."Bidirectional";
+			push(@results,$result);
+		}
+	}elsif($distance == 0){                         #c3 and c4 and c5
+		if ($gene_dir{$smname} ne $data[6]){          #c3
+			$result = $linc."\t"."Antisense";
+			push(@results,$result);
+		}else{                                        #c4 and c5
+			my $m = 0;
+			foreach my $gename(keys %gene_data){
+				if($gename eq $smname){
+					my @num = @{$gene_data{$gename}};
+					for (my $i =0;$i <= $#num;$i++){
+						if(($num[$i][0] < $data[4])&&($num[$i][1] > $data[3])){
+							$m++;
+						}
+					}
+				}
+			}
+			if ($m > 0){
+				$result = $linc."\t"."Exonic Sense";
+				push(@results,$result);
+			}else{
+				$result = $linc."\t"."Intronic Sense";
+				push(@results,$result);
+			}
+		}
+	}
+}
+my %hash;@results = grep { ! $hash{$_} ++ } @results;
+foreach my $result(@results){
+	print OUT $result."\n";
+}