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1 #!/bin/bash
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2 dir="$(cd "$(dirname "$0")" && pwd)"
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3
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4 input=$1
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5 noparse=$2
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6 scores=$3
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7 regions=$4
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8 output=$5
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9
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10 if [ "true" == "$noparse" ] ; then
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11 noparse="--noparse"
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12 else
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13 noparse=""
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14 fi
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15
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16 if [ "true" == "$scores" ] ; then
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17 scores="--scores"
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18 else
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19 scores=""
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20 fi
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21
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22 if [ "true" == "$regions" ] ; then
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23 regions="--regions"
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24 else
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25 regions=""
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26 fi
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27
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28 mkdir $PWD/outdir
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29
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30 echo "`which python3`"
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31
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32 python3 $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
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33 #/data/users/david/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
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34 #/home/galaxy/anaconda3/bin/python $dir/MakeDb.py imgt -i $input --outdir $PWD/outdir --outname output $noparse $scores $regions
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35
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36 mv $PWD/outdir/output_db-pass.tab $output
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