Mercurial > repos > biomonika > primer_tester

changeset 0:1e22519d75ac draft

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Uploaded
author biomonika
date Fri, 25 Jul 2014 17:09:47 -0400
parents
children 3a58793617ef
files primer_tester.sh
diffstat 1 files changed, 22 insertions(+), 0 deletions(-) [+]
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line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/primer_tester.sh	Fri Jul 25 17:09:47 2014 -0400
@@ -0,0 +1,22 @@
+#!/bin/bash
+primers_file=$1;
+results=$2;
+
+cat $primers_file | cut -f1 >primers_names;
+echo "primer Gorilla_female human_Y chimp_Y" >$results;
+
+while read primer
+	do
+	echo  -n $primer >>$results;
+		for dataset in ${@:3}
+		do
+			search=$(cat $dataset| grep -B 1 "Amplimer 1" | grep "Primer" | grep $primer)
+			if [ "$search" == "" ]
+			then
+				echo -n " NO" >>$results;
+			else
+				echo -n  " YES" >>$results;
+			fi
+		done
+	echo >>$results;
+done < primers_names
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