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1 #!/bin/bash
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2
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3 echo $@
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4
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5 FWDFILE=$1
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6 shift
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7 REVFILE=$1
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8 shift
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9 OUTXML=$1
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10 shift
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11 OUTCSV=$1
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12 shift
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13 ORGANISM=$1
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14
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15 OUTFOLDER=$(mktemp -d --tmpdir tmpMOST_XXXXXXXXXXXXXXXXXXXX)
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16 rm -rf $OUTFOLDER # MOST insists on creating the folder itself
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17
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18 CMD="MOST.py -1 $FWDFILE -2 $REVFILE -o $OUTFOLDER -st $ORGANISM"
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19
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20 echo $CMD
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21 eval $CMD
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22
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23 STEM=$(basename $FWDFILE)
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24 STEM="${STEM%.*}"
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25
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26 mv $OUTFOLDER"/"$STEM"_MLST_result.csv" $OUTCSV
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27 mv "$OUTFOLDER/$STEM.results.xml" $OUTXML
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28
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29 rm -rf $OUTFOLDER
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