--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/genecentrico.pl	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,101 @@
+#! /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.
+
+
+$file_all=$ARGV[0];
+$file_sub=$ARGV[1];
+$down=$ARGV[2];
+$up=$ARGV[6];
+$scelta=$ARGV[3];
+$result=$ARGV[4];
+$output=$ARGV[5];
+
+
+open(FILESUB, "<$file_sub") or die "Cannot find file $file_sub\n";
+open(FILEALL, "<$file_all") or die "Cannot open file $file_all: $!\n";
+open(FILEOUT, ">$output") or die "Cannot create file $output: $!\n";
+
+print "Analysis Type=$scelta, Promoter def:$down/$up, output=$result\n";
+
+@sub=<FILESUB>;
+@all=<FILEALL>;
+foreach $lines_all(@all){
+	chomp $lines_all;
+	#chop $lines_all;
+	if ($lines_all=~/#/g){next;}
+	@line_all=split("\t",$lines_all);
+	$chr=$line_all[2];
+	$refseq=$line_all[1];
+	$refStart=$line_all[3];
+	$refStop=$line_all[4];
+	$name=$line_all[0];
+	#$exon_count=$line_all[8];
+	#@exonStart=split(",",$line_all[9]);
+	#@exonStop=split(",",$line_all[10]);
+	$strand=$line_all[5];
+	if ($scelta eq "promoter"){
+		if ($strand eq "+"){
+			$prom_start=$refStart+$down;
+			$prom_stop=$refStart+$up;
+		}
+		if ($strand eq "-"){
+			$prom_start=$refStop-$up;
+			$prom_stop=$refStop-$down;
+		}
+	}
+	if ($scelta eq "all"){
+		if ($strand eq "+"){
+			$prom_start=$refStart+$down;
+			$prom_stop=$refStop;
+		}
+		if ($strand eq "-"){
+			$prom_start=$refStart;
+			$prom_stop=$refStop-$down;
+		}
+	}
+	
+	
+	
+	@promotore=();
+	$max_prom=0;
+	foreach $lines_sub(@sub){
+		chomp $lines_sub;
+		if ($lines_sub=~/#/g){next;}
+		@line_sub=split("\t",$lines_sub);
+		$chr_p=$line_sub[0];
+		$peakStart=$line_sub[3];
+		$peakStop=$line_sub[4];
+		$value=$line_sub[5];
+		#print "$peakStart\t$peakStop\t$prom_start\t$prom_stop\n";
+		#print "$refStart\t$refStop\t$peakStart\t$peakStop\n";
+		if (((($peakStart>=$prom_start) && ($peakStart<=$prom_stop)) || (($peakStart<=$prom_start) && ($peakStop>=$prom_start))) && ("$chr" eq "$chr_p")){
+			push(@promotore,$value);
+			#print "cazzo";
+			
+		}
+	}
+	$i=0;
+	foreach $valore(@promotore){
+		$i++;
+		if($max_prom<$valore){
+			$max_prom=$valore;
+		}
+	}
+	if ($result eq "max_value"){
+		print FILEOUT "$lines_all\t$max_prom\n";
+	}
+	else{
+		print FILEOUT "$lines_all\t$i\n";
+	}
+}