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1 #!/bin/bash
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2
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3 my_func(){
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4
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5 ind1=$(($1*2-1))
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6 ind2=$(($1*2))
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7
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8 aln1=$(echo $4 | awk -v var="$ind1" '{print $var}')
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9 aln2=$(echo $4 | awk -v var="$ind2" '{print $var}')
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10 oName=$(echo $5 | awk -v var="$1" '{print $var}')
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11
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12 echo "Merging $aln1.aln and $aln2.aln into $oName.aln"
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13
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14 l1=$(grep -c ">" $aln1.aln)
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15 l2=$(grep -c ">" $aln2.aln)
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16
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17 if [ $l1 -eq "1" ] && [ $l2 -eq "1" ]
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18 then
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19 cat $aln1.aln $aln2.aln > temp.$6.$1.fas
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20 mafft --localpair --preservecase --thread $2 --maxiterate $3 temp.$6.$1.fas > $oName.aln
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21 elif [ $l1 -eq "1" ]
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22 then
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23 mafft --preservecase --thread $2 --maxiterate $3 --addfragments $aln1.aln $aln2.aln > $oName.aln
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24 elif [ $l2 -eq "1" ]
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25 then
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26 mafft --preservecase --thread $2 --maxiterate $3 --addfragments $aln2.aln $aln1.aln > $oName.aln
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27 else
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28 cat $aln1.aln $aln2.aln > input.$6.$1.fas
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29 str1=""
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30 count=1
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31 gap=" "
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32
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33 for i in $(seq 1 1 $l1)
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34 do
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35 str1=$str1$count$gap
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36 count=$(($count+1))
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37 done
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38
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39 echo $str1 > msaTable.$6.$1
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40 str2=""
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41 for i in $(seq 1 1 $l2)
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42 do
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43 str2=$str2$count$gap
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44 count=$(($count+1))
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45 done
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46
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47 echo $str2 >> msaTable.$6.$1
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48 mafft --preservecase --thread $2 --maxiterate $3 --merge msaTable.$6.$1 input.$6.$1.fas > $oName.aln
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49
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50 fi
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51
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52 }
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53
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54 export -f my_func
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55
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56 parallel -j 1 my_func ::: $(seq 1 1 1) ::: 1 ::: 1 ::: "NODE_1 NODE_2" ::: "NODE_0" ::: "merge"
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