diff test-data/files/mergeParallel.sh @ 0:9a3a2e04f47a draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/files/mergeParallel.sh	Mon Jun 10 16:04:10 2019 -0400
@@ -0,0 +1,56 @@
+#!/bin/bash
+
+my_func(){
+
+	ind1=$(($1*2-1))
+	ind2=$(($1*2))
+
+	aln1=$(echo $4 | awk -v var="$ind1" '{print $var}')
+	aln2=$(echo $4 | awk -v var="$ind2" '{print $var}')
+	oName=$(echo $5 | awk -v var="$1" '{print $var}')
+
+	echo "Merging $aln1.aln and $aln2.aln into $oName.aln"
+
+	l1=$(grep -c ">" $aln1.aln)
+	l2=$(grep -c ">" $aln2.aln)
+
+	if [ $l1 -eq "1" ] && [ $l2 -eq "1" ] 
+	then
+		cat $aln1.aln $aln2.aln > temp.$6.$1.fas
+		mafft --localpair --preservecase --thread $2 --maxiterate $3 temp.$6.$1.fas > $oName.aln
+	elif [ $l1 -eq "1" ] 
+	then
+		mafft --preservecase --thread $2 --maxiterate $3 --addfragments $aln1.aln $aln2.aln > $oName.aln
+	elif [ $l2 -eq "1" ] 
+	then
+		mafft --preservecase --thread $2 --maxiterate $3 --addfragments $aln2.aln $aln1.aln > $oName.aln
+	else
+		cat $aln1.aln $aln2.aln > input.$6.$1.fas
+		str1=""
+		count=1
+		gap=" "
+
+		for i in $(seq 1 1 $l1)
+		do
+			str1=$str1$count$gap
+			count=$(($count+1))
+		done
+
+		echo $str1 > msaTable.$6.$1
+		str2=""
+		for i in $(seq 1 1 $l2)
+		do
+			str2=$str2$count$gap
+			count=$(($count+1))
+		done
+
+		echo $str2 >> msaTable.$6.$1
+		mafft --preservecase --thread $2 --maxiterate $3 --merge msaTable.$6.$1 input.$6.$1.fas > $oName.aln
+
+	fi
+
+}
+
+export -f my_func
+
+parallel -j 1 my_func ::: $(seq 1 1 1) ::: 1 ::: 1 ::: "NODE_1 NODE_2" ::: "NODE_0" ::: "merge"