diff scripts/number_of_not_uniq_mapped_reads.sh @ 9:695d28139f3e

toolshed8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/number_of_not_uniq_mapped_reads.sh	Tue Sep 09 14:31:02 2014 -0400
@@ -0,0 +1,53 @@
+#!/bin/bash
+#sort_into_categories $contig
+#family member with the biggest number of not uniquely mapped reads reported
+
+dir=$1;
+contig=$2;
+
+all_unmapped1=`grep $contig statistics/stat_mother | cut -f 3`; 
+high_qual_unmapped1=`grep $contig statistics/stat_mother_high | cut -f 3`; 
+diff_mother1=`expr $all_unmapped1 - $high_qual_unmapped1`;
+percentage1=`echo "scale=3; $diff_mother1/$all_unmapped1*100" | bc`;
+
+all_unmapped2=`grep $contig statistics/stat_father | cut -f 3`; 
+high_qual_unmapped2=`grep $contig statistics/stat_father_high | cut -f 3`; 
+diff_mother2=`expr $all_unmapped2 - $high_qual_unmapped2`;
+percentage2=`echo "scale=3; $diff_mother2/$all_unmapped2*100" | bc`;
+
+all_unmapped3=`grep $contig statistics/stat_daughter | cut -f 3`; 
+high_qual_unmapped3=`grep $contig statistics/stat_daughter_high | cut -f 3`; 
+diff_mother3=`expr $all_unmapped3 - $high_qual_unmapped3`;
+percentage3=`echo "scale=3; $diff_mother3/$all_unmapped3*100" | bc`;
+
+all_unmapped4=`grep $contig statistics/stat_son | cut -f 3`; 
+high_qual_unmapped4=`grep $contig statistics/stat_son_high | cut -f 3`; 
+diff_mother4=`expr $all_unmapped4 - $high_qual_unmapped4`;
+percentage4=`echo "scale=3; $diff_mother4/$all_unmapped4*100" | bc`;
+
+#searching for maximum - family member that has the biggest number of NOT uniquely mapped reads
+    if (( $(echo "$percentage1 > $percentage2"|bc -l) ));
+    	then
+        	max1="$percentage1";
+    	else
+		max1="$percentage2";
+    fi
+
+    if (( $(echo "$percentage3 > $percentage4"|bc -l) ));
+    	then
+        	max2="$percentage3";
+    	else
+		max2="$percentage4";
+    fi
+
+
+    if (( $(echo "$max1 > $max2"|bc -l) ));
+    	then
+        	percentage="$max1";
+    	else
+		percentage="$max2";
+    fi
+
+echo $percentage;
+
+