diff igblast/igblast.sh @ 53:0ef7f80ea061 draft

Uploaded

--- a/igblast/igblast.sh	Thu Feb 25 13:36:15 2021 +0000
+++ b/igblast/igblast.sh	Thu Feb 25 13:39:50 2021 +0000
@@ -1,28 +1,28 @@
-set -e
-
-dir="$(cd "$(dirname "$0")" && pwd)"
-
-input=$1
-species=$2
-locus=$3
-output=$4
-
-declare -A speciesdict
-
-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")
-
-echo "Species: $species ${speciesdict[$species]}"
-
-species="${speciesdict[$species]}"
-
-if [ "$species" == "" ]
-then
-	>&2 echo "Species not possible with igBLASTn, use IMGT"
-	exit 1
-fi
-
-echo "$input $species $locus $output"
-
-java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
-
-Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1
+set -e
+
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+input=$1
+species=$2
+locus=$3
+output=$4
+
+declare -A speciesdict
+
+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")
+
+echo "Species: $species ${speciesdict[$species]}"
+
+species="${speciesdict[$species]}"
+
+if [ "$species" == "" ]
+then
+	>&2 echo "Species not possible with igBLASTn, use IMGT"
+	exit 1
+fi
+
+echo "$input $species $locus $output"
+
+java -Xmx16G -jar $IGBLASTWRP/igblastwrp.jar -p 4 -S $species -R $locus ${input} $PWD/blasted_output 2>&1
+
+Rscript --verbose $dir/igblast.r "$PWD/blasted_output.L2.txt" "$output" 2>&1