view primer_tester.sh @ 1:3a58793617ef draft default tip

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author biomonika
date Fri, 25 Jul 2014 17:11:18 -0400
parents 1e22519d75ac
children
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#!/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