Fix appenddbtoindex check for existence by replacing grep with awk call

steineggerlab · Sep 9, 2023 · ef4e960 · ef4e960
1 parent e5339e1
commit ef4e960
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/data/structureindex.sh b/data/structureindex.sh
@@ -41,13 +41,13 @@ fi
     || fail "createindex died"
 
 if [ -n "$INCLUDE_CA" ]; then
-    if ! grep -q "^${INDEX_DB_CA_KEY_DB1}\t" "${DB}.idx.index"; then
+    if [ -z "$(awk -v key="${INDEX_DB_CA_KEY_DB1}" '$1 == key;' "${DB}.idx.index")" ]; then
         # shellcheck disable=SC2086
         "$MMSEQS" appenddbtoindex "${DB}_ca" "${DB}.idx" --id-list ${INDEX_DB_CA_KEY_DB1} ${VERBOSITY_PAR} \
             || fail "appenddbtoindex died"
     fi
     if [ -f "${DB}_seq_ca.dbtype" ] && [ "$IS_CLUDDB" = "1" ]; then
-        if ! grep -q "^${INDEX_DB_CA_KEY_DB2}\t" "${DB}.idx.index"; then
+        if [ -z "$(awk -v key="${INDEX_DB_CA_KEY_DB2}" '$1 == key;' "${DB}.idx.index")" ]; then
             # shellcheck disable=SC2086
             "$MMSEQS" appenddbtoindex "${DB}_seq_ca" "${DB}.idx" --id-list ${INDEX_DB_CA_KEY_DB2} ${VERBOSITY_PAR} \
                 || fail "appenddbtoindex died"