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2
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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
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5 ids=$2
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6 ref=$3
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7 output=$4
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8
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9 input=($input)
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10
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11 ids=($ids)
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12
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13 first="${input[0]}"
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14
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15 count=0
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16 for current in ${input[@]}
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17 do
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18 f=$(file $current)
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19 zipType="Zip archive"
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20 if [[ "$f" == *"$zipType"* ]]
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21 then
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22 id=${ids[$count]}
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23 unzip $current -d $PWD/$id/ >> $PWD/unziplog.log
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24 filename="$PWD/gappednt_${id}.txt"
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25 cat $PWD/$id/*/2_* | cut -f2,4,7 > $filename
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26 python $dir/script_imgt.py --input $filename --ref $ref --output $output --id $id
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27 else
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28 python $dir/script_xlsx.py --input $current --ref $ref --output $output
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29 fi
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30 count=$((count+1))
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31 done
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32
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