diff snpEff_2_1a/scripts/randBedIntervals.pl @ 0:f8eaa3f8194b default tip

Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/scripts/randBedIntervals.pl	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,36 @@
+#!/usr/bin/perl
+
+# Number of intervals per chromosome
+$intsPerChr = 10;
+
+# Max interval len
+$maxLen = 1000;
+
+# Chromosome length
+$len{'chr2L'} = 23299195;
+$len{'chr2LHet'} = 373492;
+$len{'chr2R'} = 21411048;
+$len{'chr2RHet'} = 3329880;
+$len{'chr3L'} = 24850358;
+$len{'chr3LHet'} = 2587444;
+$len{'chr3R'} = 28253873;
+$len{'chr3RHet'} = 2548985;
+$len{'chr4'} = 1368761;
+$len{'chrdmel_mitochondrion_genome'} = 19790;
+$len{'chrUextra'} = 29367225;
+$len{'chrU'} = 10174655;
+$len{'chrX'} = 22703118;
+$len{'chrXHet'} = 206671;
+$len{'chrYHet'} = 351384;
+
+foreach $chr ( sort keys %len ) {
+	$max = $len{$chr} - $maxLen - 1000;
+
+	for( $i=0 ; $i < $intsPerChr ; $i++ ) {
+		$start = int( rand() * $max );
+		$end = int( rand() * $maxLen ) + $start;
+
+		print "$chr\t$start\t$end\n";
+	}
+}
+