changeset 1:eaf2e2b19e41 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCentralRegions.pl	Tue Jan 05 09:13:56 2016 -0500
@@ -0,0 +1,87 @@
+#!/usr/bin/perl -w
+use strict;
+
+#creats a BED file with central area of peaks
+
+
+my $usage = qq{
+    $0
+
+    -----------------------------
+    mandatory parameters:
+    
+    -f   filename 	file with sites in BED format
+    -l   value	 	length of the cental regions
+    
+    -----------------------------
+    optional parameters:
+    -v				for verbose   
+    -head	1/0		if there is a header
+    -o		filename	output file
+};
+
+if(scalar(@ARGV) <2){
+    print $usage;
+    exit(0);
+}
+
+my $flank = 0;
+my $ResFilename = "";
+my $file = "";
+my $header = 0;
+my $verbose = 0;
+
+while(scalar(@ARGV) > 0){
+    my $this_arg = shift @ARGV;
+    if ( $this_arg eq '-h') {print "$usage\n"; exit; }
+    elsif ( $this_arg eq '-f') {$file = shift @ARGV;}
+    elsif ( $this_arg eq '-v') {$verbose = 1;}  
+    elsif ( $this_arg eq '-head') {$header = shift @ARGV;}
+    elsif ( $this_arg eq '-o') {$ResFilename = shift @ARGV;}
+    elsif ( $this_arg eq '-l') {$flank = shift @ARGV;$flank /=2;}   
+    elsif ( $this_arg =~ m/^-/ ) { print "unknown flag: $this_arg\n";}
+}
+
+
+
+
+my $count = 0;
+my %hash;
+
+open (FILE, "<$file") or die "Cannot open file $file!!!!: $!";
+open (OUT, ">$ResFilename") or die "Cannot open file $ResFilename!!!!: $!";
+
+if ($header) {
+<FILE>;
+}
+
+while (<FILE>) {		
+	s/\R//g; 
+	next if (/^#/);
+	next if (/track/);
+	next if (/summit/);
+        my @a = split /\s/;
+        my $chr = $a[0];
+        my $maxPos =  $a[3];
+        my $score = $a[4];
+	if ($maxPos=~/\D/) {
+		$maxPos = int(($a[1]+$a[2])/2);
+	} elsif ($maxPos < $a[1]){ #MACS intervals
+		$maxPos = $a[1]+$a[4];
+		$score = $a[5];
+	}
+        my $firstPos = $maxPos-$flank;
+        my $lastPos = $maxPos+$flank;
+
+        my $ID=$chr.":".$firstPos."_".$lastPos."_".$score ;
+        unless (exists($hash{$ID})) {
+            $hash{$ID}=1;
+            $count++;            
+            print OUT "$chr\t$firstPos\t$lastPos\t$score\n";
+        }
+}
+    
+#print "$file\t$count\n";
+close FILE;
+close OUT;
+