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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 ref=$2
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6 output=$3
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7 f=$(file $input)
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8 zipType="Zip archive"
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9 if [[ "$f" == *"$zipType"* ]]
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10 then
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11 echo "Zip archive, assuming IMGT output file"
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12 echo "Trying: unzip $input -d $PWD/files/"
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13 unzip $input -d $PWD/files/ > $PWD/unziplog.log
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14 cat $PWD/files/*/2_* | cut -f2,4,7 > $PWD/gappednt.txt
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15 python $dir/script_imgt.py --input $PWD/gappednt.txt --ref $ref --output $output
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16 else
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17 python $dir/script_xlsx.py --input $input --ref $ref --output $output
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18 fi
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