added (hidden) parameters to change hhblits arguments

profileview-build

@@ -25,6 +25,12 @@ trap ctrl_c INT; function ctrl_c() { exit 5; }
 
 # Definition of functions and global variables specific to this script
 
+HHBLITS_ARG_COV=70
+HHBLITS_ARG_QID=60
+HHBLITS_ARG_MAXID=98
+HHBLITS_ARG_ITER=3
+HHBLITS_ARG_EVALUE=1e-10
+
 PVLIB_FORCE=false
 PVLIB_PATH=""
 PVLIB_DOMID=""
@@ -60,7 +66,7 @@ function print_usage() {
 
 # retrieve provided arguments
 opts="i:D:d:n:t:j:hV"
-longopts="input:,domain-id:,db:,lib-name:,force,threads:,max-jobs:,help,version"
+longopts="input:,domain-id:,db:,lib-name:,force,threads:,max-jobs:,help,version,cov:,qid:,max-id:,evalue:,iter:"
 ARGS=$(getopt -o "${opts}" -l "${longopts}" -n "${CMD_NAME}" -- "${@}")
 if [ $? -ne 0 ] || [ $# -eq 0 ]; then # do not change the order of this test!
     print_usage
@@ -106,6 +112,26 @@ while [ -n "${1}" ]; do
             print_version
             exit 0
             ;;
+        --cov)
+            shift
+            HHBLITS_ARG_COV=${1}
+            ;;
+        --qid)
+            shift
+            HHBLITS_ARG_QID=${1}
+            ;;
+        --max-id)
+            shift
+            HHBLITS_ARG_MAXID=${1}
+            ;;
+        --evalue)
+            shift
+            HHBLITS_ARG_EVALUE=${1}
+            ;;
+        --iter)
+            shift
+            HHBLITS_ARG_ITER=${1}
+            ;;
         --)
             shift
             break
@@ -193,7 +219,7 @@ for query in "${PVLIB_QUERY}"/*.fa; do
     [ -e "${query}" ] || continue
     queryBase=${query##*/}
     queryName=${queryBase%.fa}
-    echo "hhblits ${HHBLITS_DBS} -i ${query} -o stdout -oa3m ${PVLIB_PREFIX}/a3m/${queryName}.a3m -ohhm ${PVLIB_PREFIX}/hhm/${queryName}.hhm -M first -qid 60 -cov 70 -id 98 -e 1e-10 -n 2 -cpu ${NTHREADS} -v 0 >/dev/null 2>&1"
+    echo "hhblits ${HHBLITS_DBS} -i ${query} -o stdout -oa3m ${PVLIB_PREFIX}/a3m/${queryName}.a3m -ohhm ${PVLIB_PREFIX}/hhm/${queryName}.hhm -M first -cov ${HHBLITS_ARG_COV} -qid ${HHBLITS_ARG_QID} -id ${HHBLITS_ARG_MAXID} -e ${HHBLITS_ARG_EVALUE} -n ${HHBLITS_ARG_ITER} -cpu ${NTHREADS} -v 0 >/dev/null 2>&1"
 done | ${PEXEC_CMD} # left it unquoted!
 
 print_status "formatting a3m files"
@@ -220,7 +246,7 @@ print_status "generating ProfileView library data"
 for hmm in "${PVLIB_DIR}"/hmm/*.hmm; do
     [ -e "${hmm}" ] || continue
     awk -v domId="${PVLIB_DOMID}" '$1~/^NAME$/{hmm_name=$2;next} $1~/^LENG$/{hmm_len=$2;next} $1~/^NSEQ$/{hmm_nseq=$2;next} $1~/^HMM$/{ OFS=","; print hmm_name,domId,hmm_nseq,hmm_len }' ${hmm}
-done > "${PVLIB_PREFIX}"/"${PVLIB_NAME}".models.list
+done > "${PVLIB_PREFIX}/${PVLIB_NAME}.models.list"
 
 python3 "${SCRIPTS_DIR}"/createHHdict.py --hhm-dir "${PVLIB_DIR}/hhm" --prefix "${PVLIB_DIR}"/${PVLIB_NAME}.hhdict >/dev/null 2>&1
 python3 "${SCRIPTS_DIR}"/createHmmerDict.py --hmm-dir "${PVLIB_DIR}/hmm" --prefix "${PVLIB_DIR}"/${PVLIB_NAME}.hmmdict >/dev/null 2>&1