Merge multiple SSMs into a single one

merge_ssms.sh

#!/bin/bash

set -e

cat helpers/triplets.lst |while read patient
do
	mergedFile=ssms/merged/${patient}.txt
	cat helpers/ssm_header.txt > ${mergedFile}

	count=0

	files=$(ls ssms/filled_in/${patient}*.txt)
	cat $files |grep -v "gene" |cut -f2 |sort |uniq -c |awk '{ if($1 > 1) print $2 }' |while read mutation
	do
		a=$(cat $files |grep "${mutation}" |cut -f3 |tr "\n" "," |sed -e 's/,$//g')
		d=$(cat $files |grep "${mutation}" |cut -f4 |tr "\n" "," |sed -e 's/,$//g')

		echo -ne "s${count}\t${mutation}\t${a}\t${d}\t0.999\t0.499\n" >> ${mergedFile}

		let count=$count+1
	done

	echo "${patient} done... [`date`]"
done