--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/calcolo_p_v4_norm_intron.pl	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,636 @@
+#! /usr/bin/perl
+
+# Copyright 2009 Matteo Cesaroni, Lucilla Luzi
+#
+# This program is free software; ; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or (at your
+# option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+
+
+#prende tutte le probes che mecciano almeno in parte dentro gli esoni
+
+use Statistics::PointEstimation;
+use Statistics::TTest;
+#use Statistics::Test::WilcoxonRankSum;
+use Getopt::Long;
+
+GetOptions ( 
+			"help"	=> \$OPT{help},
+			"ann=s" => \$OPT{ann},
+			"wt=s" => \$OPT{wt},
+			"treat=s" => \$OPT{treat},
+			"out=s" =>  \$OPT{out},
+			"pv=s" => \$OPT{prob},
+			"rc=s" => \$OPT{raw_cut},
+			"fc=s" => \$OPT{fc_cut},
+			"exon=s" => \$OPT{exon},
+			"opt=s" => \$OPT{option},
+			"norm=s" =>\$OPT{norm_q},
+			"sum_met=s" =>\$OPT{sum_met},
+			"fdr=s" =>\$OPT{fdr},
+			"log=s" =>\$OPT{log_t},
+)|| printusage(); 
+
+# opzioni da linea di comando
+my $file_ann=$OPT{ann};
+my $file_wt=$OPT{wt};
+my $file_treat=$OPT{treat};
+my $file_output=$OPT{out};
+my $pv_cut=$OPT{prob};
+my $media_cut=$OPT{raw_cut};
+my $FC_cut=$OPT{fc_cut};
+my $tipo=$OPT{exon};
+my $option=$OPT{option};
+my $normalization_q=$OPT{norm_q};
+my $sum_meth=$OPT{sum_met};
+my $corretction=$OPT{fdr};
+my $data_log=$OPT{log_t};
+
+$help and printusage(); 
+
+
+if($option eq "comp"){
+if ($sum_meth eq "both"){
+$header=<<e0c6654;
+\# annotation_file: $file_ann
+\# wt_file: $file_wt
+\# treat_file: $file_treat
+\# p-value cutoff: $pv_cut
+\# raw data cutoff cutoff: $media_cut
+\# summary method: $sum_meth
+\# fold change cutoff: $FC_cut
+\# type of analysis: $tipo
+\# headers: name RefSeq Chr txStart txEnd strand mean_chip1 mean_chip2 FC_mean median_chip1 median_chip2 FC_median num_probes_in_gene p-value FDR(q-value)
+e0c6654
+
+}
+if ($sum_meth eq "mean"){
+$header=<<e0c6654;
+\# annotation_file: $file_ann
+\# wt_file: $file_wt
+\# treat_file: $file_treat
+\# p-value cutoff: $pv_cut
+\# raw data cutoff cutoff: $media_cut
+\# summary method: $sum_meth
+\# fold change cutoff: $FC_cut
+\# type of analysis: $tipo
+\# headers: name RefSeq Chr txStart txEnd strand mean_chip1 mean_chip2 FC_mean num_probes_in_gene p-value FDR(q-value)
+e0c6654
+
+}
+if ($sum_meth eq "median"){
+$header=<<e0c6654;
+\# annotation_file: $file_ann
+\# wt_file: $file_wt
+\# treat_file: $file_treat
+\# p-value cutoff: $pv_cut
+\# raw data cutoff cutoff: $media_cut
+\# summary method: $sum_meth
+\# fold change cutoff: $FC_cut
+\# type of analysis: $tipo
+\# headers: name RefSeq Chr txStart txEnd strand median_chip1 median_chip2 FC_median num_probes_in_gene p-value FDR(q-value)
+e0c6654
+
+}
+
+
+
+# "usage" se non ci sono opzioni
+if (!$file_ann || !$file_wt || !$file_treat) {
+	&printusage()
+}
+
+#if ($pv_cut == 1){$pv_cut=0.9999;}
+if (!$media_cut){$media_cut=0;}
+if (!$FC_cut){$FC_cut=0;}
+
+my @r1=();
+my @r2=();
+
+#my $confident=(1-$pv_cut)*100;
+#inserire nell'ordine: tabella annotazione, tabella valori wt, tabella valori treated, p-value cutoff, raw signal cutoff
+
+
+open (annotation,"<$file_ann") || die "file_ann not open:$!\n";
+open (wt,"<$file_wt") || die "$file_wt not open:$!\n";
+open (treated,"<$file_treat") || die "$file_treat not open:$!\n";
+open (output,">$file_output") || die "bed_$file_wt not open:$!\n";
+
+print output "$header";
+
+print "Comparison --> probe_selection=$tipo, Normalization=$normalization_q, summary method=$sum_meth Filters: p-value=$pv_cut, raw value=$media_cut, FC=$FC_cut";
+
+while (defined (my $line_down = <annotation>)) {
+   chomp $line_down;
+   my @tmp_down = split("\t", $line_down);
+   my @probe_match=split("\,", $tmp_down[9]);
+   foreach $probes (@probe_match){
+   		my @coord=split("-", $probes);
+   		$tab_tot{$tmp_down[0]}{"$coord[0]\t$coord[1]"}.="$tmp_down[1]\n$tmp_down[7]\n$tmp_down[0]\n$tmp_down[2]\n$tmp_down[3]\n$tmp_down[4]\n$tmp_down[5]\n$tmp_down[6]\n"; 
+   		push(@ciclo,"$tmp_down[0]\t$coord[0]\t$coord[1]");
+   }	 
+} 
+
+while (defined (my $line_down = <wt>)) {
+   chomp $line_down;
+   my @tmp_down = split("\t", $line_down);  
+   chomp $tmp_down[0];
+   $tab_tot_wt{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
+}
+
+
+while (defined (my $line_down = <treated>)) {
+   chomp $line_down;
+   my @tmp_down = split("\t", $line_down); 
+   chomp $tmp_down[0];
+   $tab_tot_treat{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
+}
+
+if($normalization_q eq "yes"){
+
+	@sort_wt=sort{$tab_tot_wt{$a} <=> $tab_tot_wt{$b}} keys %tab_tot_wt;
+	@sort_treat=sort{$tab_tot_treat{$a} <=> $tab_tot_treat{$b}} (keys %tab_tot_treat);
+
+	for($i=0;$i<=$#sort_wt;$i++){
+		$media=($tab_tot_wt{$sort_wt[$i]}+$tab_tot_treat{$sort_treat[$i]})/2;
+		$tab_tot_value{$sort_wt[$i]}.="$media\n";
+	}
+
+	for($i=0;$i<=$#sort_treat;$i++){
+		$media=($tab_tot_wt{$sort_wt[$i]}+$tab_tot_treat{$sort_treat[$i]})/2;
+		$tab_tot_value{$sort_treat[$i]}.="$media\n";
+	}
+
+}
+
+
+foreach $key_value(@ciclo){
+			
+			@keys_values=split("\t",$key_value);
+			@array1= split("\n",$tab_tot{$keys_values[0]}{"$keys_values[1]\t$keys_values[2]"});
+			if($normalization_q eq "yes"){
+				@array2= split("\n",$tab_tot_value{"$keys_values[1]\t$keys_values[2]"});
+				$value1=$array2[0];
+				$value2=$array2[1];
+			}
+			else{
+				$value1=$tab_tot_wt{"$keys_values[1]\t$keys_values[2]"};
+				$value2=$tab_tot_treat{"$keys_values[1]\t$keys_values[2]"};
+			}
+			if ($tipo eq "internal_exon"){
+				$prendo = "^exon";
+			}
+			if ($tipo eq "all_exon"){
+				$prendo = "exon";
+			}
+			if ($tipo eq "last_exon"){
+				$prendo = "exon last";
+			}
+			
+			if ((!($array1[0] eq "")) && ($array1[1] =~ /$prendo/g))  {
+				if ($data_log eq "no_log"){
+					$log1=log($value1)/log(2);	
+					$log2=log($value2)/log(2);
+				}
+				if ($data_log eq "log"){
+					$log1=$value1;	
+					$log2=$value2;
+				}
+				$tab_gene_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
+				$tab_gene_tratted{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log2\n";
+			}	
+		
+}
+
+foreach $key (keys %tab_gene_wt) { 
+	@r1=split("\n",$tab_gene_wt{$key});
+	@r2=split("\n",$tab_gene_tratted{$key});
+	
+	sort {$a <=> $b} (@r1);
+	sort {$a <=> $b} (@r2);
+	
+	if ($#r1>0){
+		my $ttest = new Statistics::TTest;  
+ 		$ttest->set_significance(95);
+ 		$ttest->load_data(\@r1,\@r2); 
+    	my $s1=$ttest->{s1};  
+    	my $s2=$ttest->{s2};  
+		$media1=$s1->{mean};
+		$media2=$s2->{mean};
+		$total_probes=$#r1+1;
+		$potenza_a=$media2-$media1;
+		$FCa=((2)**$potenza_a);
+    	if( (@r1 % 2) == 1 ) {
+        	$median1 = $r1[((@r1+1) / 2)-1];
+        	$median2 = $r2[((@r2+1) / 2)-1];
+    	} else {
+        	$median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
+        	$median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
+	    }
+		$potenza_m=$median2-$median1;
+		$FCm=((2)**$potenza_m);
+		
+		
+		if ($FCa<1){
+			$FCa=(-(1/$FCa));
+		}
+		
+		
+		if ($FCm<1){
+			$FCm=(-(1/$FCm));
+		}
+		if ($sum_meth eq "mean"){
+			if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCa))){
+				next;
+			}
+			$p_value{"$key\t$media1\t$media2\t$FCa\t$total_probes"}=$ttest->{t_prob};
+			
+			#print output "$key\t$media1\t$media2\t$FCa\t",$ttest->{t_prob},"\t$total_probes\n";
+		}
+		if ($sum_meth eq "median"){
+			if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCm))){
+				next;
+			}
+			#print output "$key\t$median1\t$median2\t$FCm\t",$ttest->{t_prob},"\t$total_probes\n";
+			$p_value{"$key\t$median1\t$median2\t$FCm\t$total_probes"}=$ttest->{t_prob};
+		}
+		if ($sum_meth eq "both"){
+			if (($media1<$media_cut) && ($media2<$media_cut)){
+				next;
+			}
+			#print output "$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t",$ttest->{t_prob},"\t$total_probes\n";
+			$p_value{"$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t$total_probes"}=$ttest->{t_prob};
+		}
+	}
+	if ($#r1==0){
+		$media1=$r1[0];
+		$media2=$r2[0];
+		$median1=$r1[0];
+		$median2=$r2[0];
+		$potenza=$media2-$media1;
+		$FCa=((2)**$potenza);
+		$FCm=((2)**$potenza);
+		if ($FCa<1){
+			$FCa=(-(1/$FCa));	
+		}
+		if ($FCm<1){
+			$FCm=(-(1/$FCm));
+		}
+		
+		if ($sum_meth eq "both"){
+			if (($media1<$media_cut) && ($media2<$media_cut)){
+				next;
+			}
+			$p_value{"$key\t$media1\t$media2\t$FCa\t$median1\t$median2\t$FCm\t$total_probes"}=1;
+		}
+		if ($sum_meth eq "mean"){
+			if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCa))){
+				next;
+			}
+			$p_value{"$key\t$media1\t$media2\t$FCa\t$total_probes"}=1;
+		}
+		if ($sum_meth eq "median"){
+			if ((($media1<$media_cut) && ($media2<$media_cut)) || ($FC_cut>=abs($FCm))){
+				next;
+			}
+			$p_value{"$key\t$median1\t$median2\t$FCm\t$total_probes"}=1;
+		}
+	}
+}
+
+@sort_pvalue=sort{$p_value{$a} <=> $p_value{$b}} keys %p_value;
+
+if($corretction eq "yes"){
+	for($i=0;$i<=$#sort_pvalue;$i++){
+		$qvalue=$p_value{$sort_pvalue[$i]}*(($#sort_pvalue+1)/($i+1));
+		push(@QVALUE, $qvalue);
+	}
+ 
+	@qvalue_sort = sort {$a <=> $b} @QVALUE;
+
+	for($i=0;$i<=$#sort_pvalue;$i++){
+		#$FDR=((($i+1)*0.05)/($#sort_pvalue+1));
+		$qvalue=shift(@qvalue_sort);
+		if($qvalue>1){$qvalue=1;}
+		if($pv_cut>=$qvalue){
+			print output "$sort_pvalue[$i]\t$p_value{$sort_pvalue[$i]}\t$qvalue\n";
+		}
+	}
+}
+if($corretction eq "no"){
+	for($i=0;$i<=$#sort_pvalue;$i++){
+		if($pv_cut>=$qvalue){
+			print output "$sort_pvalue[$i]\t$p_value{$sort_pvalue[$i]}\n";
+		}
+	}
+}
+
+
+
+
+
+}
+if($option eq "expr"){
+if ($sum_meth eq "median"){
+$header=<<e0c6654;
+\# annotation_file: $file_ann
+\# expression_file: $file_wt
+\# type of analysis: $tipo
+\# summary method: $sum_meth
+\# headers: name RefSeq Chr txStart txEnd strand median_chip num_probes_in_gene
+e0c6654
+
+}	
+if ($sum_meth eq "mean"){
+$header=<<e0c6654;
+\# annotation_file: $file_ann
+\# expression_file: $file_wt
+\# type of analysis: $tipo
+\# summary method: $sum_meth
+\# headers: name RefSeq Chr txStart txEnd strand mean_chip num_probes_in_gene
+e0c6654
+
+}	
+if ($sum_meth eq "both"){
+$header=<<e0c6654;
+\# annotation_file: $file_ann
+\# expression_file: $file_wt
+\# type of analysis: $tipo
+\# summary method: $sum_meth
+\# headers: name RefSeq Chr txStart txEnd strand mean_chip median_chip num_probes_in_gene
+e0c6654
+
+}	
+	if (!$file_ann || !$file_wt) {
+		&printusage()
+	}
+my @r1=();
+my @r2=();
+
+
+open (annotation,"<$file_ann") || die "file_ann not open:$!\n";
+open (wt,"<$file_wt") || die "$file_wt not open:$!\n";
+open (output,">$file_output") || die "bed_$file_wt not open:$!\n";
+
+print output "$header";
+
+print "Expression --> probe_selection=$tipo summary method=$sum_meth";
+
+while (defined (my $line_down = <annotation>)) {
+   chomp $line_down;
+   my @tmp_down = split("\t", $line_down);
+   my @probe_match=split("\,", $tmp_down[9]);
+   foreach $probes (@probe_match){
+   		my @coord=split("-", $probes);
+   		$tab_tot{$tmp_down[0]}{"$coord[0]\t$coord[1]"}.="$tmp_down[1]\n$tmp_down[7]\n$tmp_down[0]\n$tmp_down[2]\n$tmp_down[3]\n$tmp_down[4]\n$tmp_down[5]\n$tmp_down[6]\n";   
+   		push(@ciclo,"$tmp_down[0]\t$coord[0]\t$coord[1]");
+   }	 
+} 
+
+while (defined (my $line_down = <wt>)) {
+   chomp $line_down;
+   $line_down=~ s/ //g;
+   my @tmp_down = split("\t", $line_down);  
+   chomp $tmp_down[0];
+   $tab_tot_wt{"$tmp_down[0]\t$tmp_down[3]"}=$tmp_down[5];
+}
+#@sort_wt=sort{$tab_tot_wt{$a} <=> $tab_tot_wt{$b}} keys %tab_tot_wt;
+
+
+#print "ciclo = $ciclo[0]\t$ciclo[1]\n";
+
+foreach $key_value(@ciclo){
+
+			@keys_values=split("\t",$key_value);
+			@array1= split("\n",$tab_tot{$keys_values[0]}{"$keys_values[1]\t$keys_values[2]"});
+			@array2= split("\n",$tab_tot_wt{"$keys_values[1]\t$keys_values[2]"});
+			
+			if ($tipo eq "internal_exon"){
+				$prendo = "^exon"; 
+			}
+			if ($tipo eq "all_exon"){
+				$prendo = "exon";
+			}
+			if ($tipo eq "last_exon"){
+				$prendo = "exon last";
+			}
+			
+			if ((!($array1[0] eq "")) && ($array1[1] =~ /$prendo/g))  {
+				
+				if ($data_log eq "no_log"){
+					$log1=log($array2[0])/log(2);
+				}
+				if ($data_log eq "log"){
+					$log1=$array2[0];
+				}
+				
+				$tab_gene_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
+			}	
+			if ((!($array1[0] eq "")) && ($array1[1] =~ /intron/g))  {
+				if ($data_log eq "no_log"){
+					$log1=log($array2[0])/log(2);
+				}
+				if ($data_log eq "log"){
+					$log1=$array2[0];
+				}	
+				$tab_intron_wt{"$array1[0]\t$array1[2]\t$array1[3]\t$array1[4]\t$array1[5]\t$array1[6]"}.="$log1\n";
+			}	
+	
+}
+
+
+foreach $key (keys %tab_gene_wt) { 
+	@r1=split("\n",$tab_gene_wt{$key});
+	if (exists $tab_intron_wt{$key}){
+		@r2=split("\n",$tab_intron_wt{$key});
+		sort {$a <=> $b} (@r2);
+	}else{
+		@r2=("no");
+	}
+	sort {$a <=> $b} (@r1);
+	if ($#r2>0) {
+		if ($#r1>0) {
+			my $ttest = new Statistics::TTest;  
+ 			$ttest->set_significance(95);
+ 			$ttest->load_data(\@r1,\@r2); 
+    		my $s1=$ttest->{s1};  
+    		my $s2=$ttest->{s2};  
+			$media1=$s1->{mean};
+			$media2=$s2->{mean};
+			$total_probes=$#r1+1;
+			$total_probes2=$#r2+1;
+    		if( (@r1 % 2) == 1 ) {
+        		$median1 = $r1[((@r1+1) / 2)-1];
+    		} else {
+        		$median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
+	    	}
+	    	if( (@r2 % 2) == 1 ) {
+        		$median2 = $r2[((@r2+1) / 2)-1];
+    		} else {
+        		$median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
+	    	}
+	    	if($media1>=$media2){
+	    		$pvalue=$ttest->{t_prob};
+	    	}
+	    	if($media1<$media2){
+	    		$pvalue=1;
+	    	}
+	    	if ($sum_meth eq "mean"){
+				print output "$key\t$media1\t$media2\t$pvalue\t$total_probes\t$total_probes2\n";
+				#print output "$key\t$media1\t$total_probes\n";
+			}
+			if ($sum_meth eq "median"){
+				print output "$key\t$median1\t$median2\t$pvalue\t$total_probes\t$total_probes2\n";
+				#print output "$key\t$median1\t$total_probes\n";
+			}
+			if ($sum_meth eq "both"){
+				print output "$key\t$media1\t$media2\t$median1\t$median2\t$pvalue\t$total_probes\t$total_probes2\n";
+				#print output "$key\t$media1\t$median1\t$total_probes\n";
+			}
+	    }
+	    if ($#r1==0) {
+			@r1=@r2;
+			my $ttest = new Statistics::TTest;  
+ 			$ttest->set_significance(95);
+ 			$ttest->load_data(\@r1,\@r2); 
+    		my $s2=$ttest->{s2};  
+			$media2=$s2->{mean};
+			$total_probes=1;
+			$total_probes2=$#r2+1;
+			$media1=$r1[0];
+			$median1=$r1[0];
+			if( (@r2 % 2) == 1 ) {
+        		$median2 = $r2[((@r2+1) / 2)-1];
+    		} else {
+        		$median2 = ($r2[(@r2 / 2)-1] + $r2[@r2 / 2]) / 2;
+	    	}
+	    	if ($sum_meth eq "mean"){
+				print output "$key\t$media1\t$media2\tNA\t$total_probes\t$total_probes2\n";
+				#print output "$key\t$media1\t$total_probes\n";
+			}
+			if ($sum_meth eq "median"){
+				print output "$key\t$median1\t$median2\tNA\t$total_probes\t$total_probes2\n";
+				#print output "$key\t$median1\t$total_probes\n";
+			}
+			if ($sum_meth eq "both"){
+				print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t$total_probes\t$total_probes2\n";
+				#print output "$key\t$media1\t$median1\t$total_probes\n";
+			}
+		}
+	    	
+		
+	}
+	
+	if ($r2[0] eq "no") {
+		if ($#r1>0) {
+			@r2=@r1;
+			my $ttest = new Statistics::TTest;  
+ 			$ttest->set_significance(95);
+ 			$ttest->load_data(\@r1,\@r2); 
+    		my $s1=$ttest->{s1};  
+			$media1=$s1->{mean};
+			$total_probes=$#r1+1;
+    		if( (@r1 % 2) == 1 ) {
+        		$median1 = $r1[((@r1+1) / 2)-1];
+    		} else {
+        		$median1 = ($r1[(@r1 / 2)-1] + $r1[@r1 / 2]) / 2;
+	   		}
+	   	}
+	   	if ($#r==0){
+	   		$media1=$r1[0];
+			$median1=$r1[0];
+			$total_probes=$#r1+1;
+	   	}
+		$media2=0;
+		$median2=0;
+		if ($sum_meth eq "both"){
+			print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t$total_probes\t0\n";
+			#print output "$key\t$media1\t$median1\t$total_probes\n";
+		}
+		if ($sum_meth eq "mean"){
+			print output "$key\t$media1\t$media2\tNA\t$total_probes\t0\n";
+			#print output "$key\t$media1\t$total_probes\n";
+		}
+		if ($sum_meth eq "median"){
+			print output "$key\t$median1\t$median2\tNA\t$total_probes\t0\n";
+			#print output "$key\t$median1\t$total_probes\n";
+		}
+	}
+	if (($#r2 == 0) && ($r2[0] ne "no") && ($#r1==0)){
+		$media1=$r1[0];
+		$media2=$r2[0];
+		$median1=$r1[0];
+		$median2=$r2[0];
+		if ($sum_meth eq "both"){
+			print output "$key\t$media1\t$media2\t$median1\t$median2\tNA\t1\t1\n";
+			#print output "$key\t$media1\t$median1\t1\n";
+		}
+		if ($sum_meth eq "mean"){
+			print output "$key\t$media1\t$media2\tNA\t1\t1\n";
+			#print output "$key\t$media1\t1\n";
+		}
+		if ($sum_meth eq "median"){
+			print output "$key\t$median1\t$median2\tNA\t1\t1\n";
+			#print output "$key\t$median1\t1\n";
+		}	
+	}		
+}
+	
+
+
+
+}
+
+
+
+
+
+####################################################################################################################################
+ 
+sub printusage {
+
+	print<<eoc22334;
+
+	
+
+	***************************************************************
+	:: N i m b l e G e n   E x p r e s s i o n   A n a l y s i s ::
+	***************************************************************
+
+
+	 USAGE SUMMARY
+     ---------------------------------------------------------------------------------
+	This program utilizes NimbleGen ratio files in gff format as INPUT FILE and 
+	provides a table of the computed picks in the same gff file format.
+	
+	
+	--ann annotation file
+	--wt wild type file
+	--treat treated file
+	--pv p-value cut-off	
+	--rc raw signal cut-off
+	--fc fold change cut-toff
+	
+     -----------------------------------------------------------------------------------------
+	 EXAMPLES:
+
+	 perl program.pl --in 75340_ratio.gff --perc 0.98 --t s --num 3 --dist 250 --w 500
+OR
+	 perl program.pl --in 75340_ratio.gff --perc 0.98 --t p --log 5 --num 3 --dist 250 --w 500
+
+     -----------------------------------------------------------------------------------------
+
+eoc22334
+	exit 0;
+ 
+}
+
+
+