diff peakfilter.pl @ 0:d42f4d78c85e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peakfilter.pl	Wed Dec 17 10:40:23 2014 -0500
@@ -0,0 +1,43 @@
+#!/usr/bin/perl
+########################################
+#### Filters peaks by p-value and width
+#### Perl script		
+#######################################
+
+
+use feature qw(say);
+
+
+# ================== 
+# Parsing Arguments
+# ================== 
+#initialize to NULL
+my $bed_file = NULL; #bed file
+
+#Parse the arguments
+$bed_file = $ARGV[0]; #bed file
+#=======================> DONE! 
+
+
+
+
+# ========================================
+# Parse the bed file and extend the reads
+# ========================================
+#open the file
+open(DATA, $bed_file) || die("Can't open the bed file, probably you gave me the wrong path!");
+
+while (<DATA>) {
+    my ($chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit, $minpeak, $geom) = split(/\t/,$_,12);
+    
+	my $size = $end - $start;
+	
+	if($size >= $minpeak) {
+		if($signal > $geom) {
+			#Now write the new line
+			$summit =~ s/\015?\012?$//;
+			say join "\t", $chr, $start, $end, $name, $score, $strand, $signal, $pvalue, $qvalue, $summit;
+		}
+	}
+}
+#=======================> DONE!