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52
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1 set -e
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2
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3 dir="$(cd "$(dirname "$0")" && pwd)"
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4
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5 input=$1
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6 species=$2
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7 locus=$3
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8 output=$4
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9
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10 declare -A speciesdict
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11
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12 speciesdict=(["Rattus norvegicus functional"]="rat" ["Rattus norvegicus non-functional"]="rat" ["Oryctolagus cuniculus functional"]="rabbit" ["Oryctolagus cuniculus non-functional"]="rabbit" ["Mus musculus functional"]="mouse" ["Mus musculus non-functional"]="mouse" ["Homo sapiens functional"]="human" ["Homo sapiens non-functional"]="human" ["Macaca mulatta non-functional"]="rhesus_monkey" ["Macaca mulatta functional"]="rhesus_monkey")
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13
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14 echo "Species: $species ${speciesdict[$species]}"
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15
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16 species="${speciesdict[$species]}"
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17
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18 if [ "$species" == "" ]
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19 then
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20 >&2 echo "Species not possible with igBLASTn, use IMGT"
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21 exit 1
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22 fi
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23
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24 echo "$input $species $locus $output"
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25
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26 java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
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27
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28 Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1
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