Check tsv file exist

genome-nexus · Aug 22, 2024 · 4577692 · 4577692
1 parent 5fd2b8b
commit 4577692
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/scripts/import_mongo.sh b/scripts/import_mongo.sh
@@ -72,6 +72,12 @@ do
 
     echo "Transforming $mutation_assessor_tsv_file"
     # Rename the columns
+    if [ -f "${DIR}/../data/common_input/${mutation_assessor_tsv_file}" ]; then
+        echo "File exists: ${DIR}/../data/common_input/${mutation_assessor_tsv_file}"
+    else
+        echo "File not found: ${DIR}/../data/common_input/${mutation_assessor_tsv_file}"
+        exit 1
+    fi
     sed -i '' 's/uniprotId\tSV\thgvspShort\tF_score\tF_impact\tMSA\tMAV/uniprotId\tsv\thgvspShort\tf_score\tf_impact\tmsa\tmav/' ${DIR}/../data/common_input/$mutation_assessor_tsv_file
     # Add a new column "_id" (uniprotId,hgvspShort)
     awk -F'\t' 'BEGIN{OFS="\t"} NR==1{print "_id",$0; next} {print $1","$3,$0}' ${DIR}/$mutation_assessor_tsv_file > ${DIR}/../data/common_input/processed_$mutation_assessor_tsv_file