ability to turn off given resources in the pipeline

assemble.sh

@@ -38,25 +38,36 @@ check_exit_code(){
 log() {
     echo `date +"%T"`: $1
 }
-# Get associations from DisGeNET
-log "Querying DisGeNET..."
-disgenet_out_path=${RES_DIR}/01-disgenet-n_${DISGENET_CNT_THRESHOLD}-s_${DISGENET_ASSOCIATION_SCORE_THRESHOLD_STR}.json
-$PYTHON_BIN $ASSOCIATIONS_DIR/disgenet.py -o ${ORPHANET_IDS} -n ${DISGENET_CNT_THRESHOLD} -s ${DISGENET_ASSOCIATION_SCORE_THRESHOLD} > ${disgenet_out_path}
-check_exit_code
-log "DisGeNET gene and variant associations stored in ${disgenet_out_path}"
 
 
-# Get associations from OpenTargets
-log "Querying OpenTargets..."
-opentargets_out_path=${RES_DIR}/01-opentargets-n_${DISGENET_CNT_THRESHOLD}-s_${OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD_STR}.json
-$PYTHON_BIN $ASSOCIATIONS_DIR/opentargets.py -o ${ORPHANET_IDS} -n ${OPENTARGETS_CNT_THRESHOLD} -s ${OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD} > ${opentargets_out_path}
-check_exit_code
-log "Opentargets gene and variant associations stored in ${opentargets_out_path}"
+out_paths=""
+if [ ${USE_DISGENET} = 1 ]; then
+    log "Querying DisGeNET..."
+    disgenet_out_path=${RES_DIR}/01-disgenet-n_${DISGENET_CNT_THRESHOLD}-s_${DISGENET_ASSOCIATION_SCORE_THRESHOLD_STR}.json
+    $PYTHON_BIN $ASSOCIATIONS_DIR/disgenet.py -o ${ORPHANET_IDS} -n ${DISGENET_CNT_THRESHOLD} -s ${DISGENET_ASSOCIATION_SCORE_THRESHOLD} > ${disgenet_out_path}
+    check_exit_code
+    log "DisGeNET gene and variant associations stored in ${disgenet_out_path}"
+    out_paths="${out_paths},${disgenet_out_path}"
+fi
+
+
+if [ ${USE_OPENTARGETS} = 1 ]; then
+    # Get associations from OpenTargets
+    log "Querying OpenTargets..."
+    opentargets_out_path=${RES_DIR}/01-opentargets-n_${DISGENET_CNT_THRESHOLD}-s_${OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD_STR}.json
+    $PYTHON_BIN $ASSOCIATIONS_DIR/opentargets.py -o ${ORPHANET_IDS} -n ${OPENTARGETS_CNT_THRESHOLD} -s ${OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD} > ${opentargets_out_path}
+    check_exit_code
+    log "Opentargets gene and variant associations stored in ${opentargets_out_path}"
+    out_paths="${out_paths},${opentargets_out_path}"
+fi
+
+
 
 # Merge with ClinVar
 log "Merging with ClinVar..."
 genes_variants_out_path=${RES_DIR}/02-genes_variants.log
-$PYTHON_BIN $ASSOCIATIONS_DIR/merge_with_clinvar.py -v $disgenet_out_path,$opentargets_out_path -c ${ASSOCIATIONS_DATA_DIR}/OrphaHPO_clinvar_variants_summary.tsv -oid ${ORPHANET_IDS} > ${genes_variants_out_path}
+out_paths=${out_paths#,}
+$PYTHON_BIN $ASSOCIATIONS_DIR/merge_with_clinvar.py -v $out_paths -c ${ASSOCIATIONS_DATA_DIR}/OrphaHPO_clinvar_variants_summary.tsv -oid ${ORPHANET_IDS} > ${genes_variants_out_path}
 check_exit_code
 log "Integration with ClinVar stored in ${genes_variants_out_path}"
 

associations/extend_network/get_extended_network.R

@@ -61,7 +61,7 @@ if (dbsource == "stringdb" | dbsource == "text_mining") {
                            filters = 'hgnc_symbol', 
                            values = input, 
                            mart = ensembl)
-  biomartCacheClear()
+
   ensprotein_idest <- subset(ensprotein_idest, ensembl_peptide_id != "")
   message(paste0("there are ", length(unique(ensprotein_idest$hgnc_symbol))), " genes in the input file with ensembl protein ids")
   
@@ -132,7 +132,7 @@ if (dbsource == "stringdb" | dbsource == "text_mining") {
                               filters = 'ensembl_peptide_id', 
                               values = protein_info, 
                               mart = ensembl)
-  biomartCacheClear()
+
   protein_info_2ensp <- subset(protein_info_2ensp, hgnc_symbol != "")
 
   ppi_network <- merge(ppi_network, protein_info_2ensp, by.x = "source", by.y = "ensembl_peptide_id" ) 

parameters.sh

+#!/usr/bin/env bash
+
 ORPHANET_IDS="130"
 #ORPHANET_IDS="851,404493,46348,85295"
 #ORPHANET_IDS="33,67046,79327,79321,86309"
 
+USE_DISGENET=1
 DISGENET_CNT_THRESHOLD=50
 DISGENET_ASSOCIATION_SCORE_THRESHOLD="0"
 
+USE_OPENTARGETS=1
 OPENTARGETS_CNT_THRESHOLD=50
 OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD="0.3"