changeset 2:cfede5ba1e76 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/createControlPeakSubSet.pl	Tue Jan 05 08:06:05 2016 -0500
@@ -0,0 +1,163 @@
+#!/usr/bin/perl
+
+#create a control dataset with the same number of reads as in the SAMPLE (highest peaks)
+
+use strict;
+use warnings;
+use diagnostics;
+
+my $usage = qq{
+    $0
+
+    -----------------------------
+    mandatory parameters:
+    
+    -f CHiP_file               	
+    -c control_file
+    -o output file
+    -----------------------------
+    optional parameters:
+
+    -n number of files to create
+    
+    none			
+};
+
+if(scalar(@ARGV) == 0){
+    print $usage;
+    exit(0);
+}
+
+## mandatory arguments
+
+my $filename = "";
+my $output_fname = "";
+
+my $controlFilename = "";
+
+my $nBootstrap = 1;
+
+
+## optional arguments
+
+## parse command line arguments
+
+while(scalar(@ARGV) > 0){
+    my $this_arg = shift @ARGV;
+    if ( $this_arg eq '-h') {print "$usage\n"; exit; }
+
+    elsif ( $this_arg eq '-f') {$filename = shift @ARGV;}
+    elsif ( $this_arg eq '-c') {$controlFilename = shift @ARGV;}
+    elsif ( $this_arg eq '-o') {$output_fname = shift @ARGV;}
+    elsif ( $this_arg eq '-n') {$nBootstrap = shift @ARGV;}
+
+    elsif ( $this_arg =~ m/^-/ ) { print "unknown flag: $this_arg\n";}
+}
+
+if ( $filename eq ""){
+    die "you should specify chip file\n";
+}
+if( $controlFilename eq ""){
+    die "you should specify control file\n";
+}
+
+if( $output_fname eq ""){
+    die "you should specify output filename\n";
+}
+
+
+print "\n-----------------\n\n";
+
+my %hash;
+my $chipCount = 0;
+my @header;
+open FILE, "< $filename " || die "$filename : $!\n";    
+while(<FILE>){
+    $chipCount++;	    
+}
+close FILE;
+#print "ChIP: $chipCount\n";
+
+
+my $controlCount = 0;
+
+open FILE, "< $controlFilename " || die "$controlFilename : $!\n";    
+while(<FILE>){
+    next if (/track/);
+    my $entry = $_;
+    my @fields = split(/\t/,$_);
+    $hash{$entry} = $fields[4]; 
+    $controlCount++;
+}
+#print "controlCount : $controlCount\n";
+
+close FILE;
+open OUT, "> $output_fname" || die "$output_fname: $!\n";
+my $count = 0;
+if ($controlCount>$chipCount) {
+    my $prob = $chipCount/$controlCount*1.1;
+    for my $entry (sort {$hash{$b}<=>$hash{$a}} keys %hash) {	
+	my $yes = rand();
+	if ($yes<=$prob) {$yes=1;}else {$yes=0;}	
+	if ($yes) {
+		print OUT $entry ;	
+		$count++;	
+	}
+	if ($count >=$chipCount) {
+	    last;
+	}
+    }
+   
+} else {    
+    for my $entry (keys %hash) {	
+	print OUT $entry;		
+    }
+}
+
+close OUT;
+
+
+for my $try (2..$nBootstrap) {
+
+	open OUT, "> $output_fname$try" || die "$output_fname$try: $!\n";
+	my $count = 0;
+	if ($controlCount>$chipCount) {
+	    my $prob = $chipCount/$controlCount*1.1;
+	    for my $entry (sort {$hash{$b}<=>$hash{$a}} keys %hash) {	
+		my $yes = rand();
+		if ($yes<=$prob) {$yes=1;}else {$yes=0;}		
+		if ($yes) {
+			print OUT $entry ;	
+			$count++;	
+		}
+		
+		if ($count >=$chipCount ) {
+		    last;
+		}
+	    }
+	    if ($count <$chipCount) { #do it again!
+
+		for my $entry (sort {$hash{$b}<=>$hash{$a}} keys %hash) {	
+			my $yes = rand();
+			if ($yes<=$prob) {$yes=1;}else {$yes=0;}		
+			if ($yes) {
+				print OUT $entry ;	
+				$count++;	
+			}
+		
+			if ($count >=$chipCount ) {
+			    last;
+			}
+	        }
+
+	    }
+	   
+	} else {    
+	    for my $entry (keys %hash) {	
+		print OUT $entry;		
+	    }
+	}
+
+	close OUT;
+
+}