ability to pass parameters to enrichment analysis from the parameters script

assemble.sh

@@ -11,6 +11,7 @@ EXTEND_CONFIG=${EXTEND_DIR}/config.txt
 RES_DIR=results
 ENRICHMENT_DIR=enrichment/
 ENRICHMENT_CONFIG=${ENRICHMENT_DIR}/config.txt
+ENRICHMENT_CONFIG_TMP=${ENRICHMENT_CONFIG}.tmp
 MAP_GENERATOR_DIR=map_generator/
 PYTHON_BIN=python3
 PIP_BIN=pip3
@@ -24,6 +25,9 @@ mkdir $RES_DIR
 RES_DIR=$RES_DIR/${ORPHANET_IDS_UNDERSCORE}
 mkdir $RES_DIR
 
+# First we copy the parameters into the result directory
+cp parameters.sh ${RES_DIR}
+
 # Get associations from DisGeNET
 disgenet_out_path=${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}
@@ -69,11 +73,21 @@ if [ ${STOP_AFTER_STAGE} = 1 ]; then
 fi
 # ------------------------------ 2. Obtain pathways ------------------------------
 echo "Retrieving enriched pathways"
-Rscript --vanilla ${ENRICHMENT_DIR}/enrich_maps.R ${genes_out_path} ${ENRICHMENT_CONFIG}
+
+tr '\r' '\n' < ${ENRICHMENT_CONFIG} > ${ENRICHMENT_CONFIG_TMP}
+
+#update paremters file
+sed -E -i "s/(max_areas_per_map)(.*)/\1\t${ENRICH_MAX_AREAS_PER_MAP}/g" ${ENRICHMENT_CONFIG_TMP}
+sed -E -i "s/(max_areas_per_pathway_db)(.*)/\1\t${MAX_AREAS_PER_PATHWAY_DB}/g" ${ENRICHMENT_CONFIG_TMP}
+
+Rscript --vanilla ${ENRICHMENT_DIR}/enrich_maps.R ${genes_out_path} ${ENRICHMENT_CONFIG_TMP}
 enriched_maps_out_path=$RES_DIR/05-enriched_disease_maps.txt
 enriched_paths_out_path=$RES_DIR/05-enriched_pathways.txt
 mv enriched_disease_maps.txt ${enriched_maps_out_path}
 mv enriched_pathways.txt ${enriched_paths_out_path}
+
+rm ${ENRICHMENT_CONFIG_TMP}
+
 echo "Enriched pathways obtained"
 
 

enrichment/config.txt

-type	resource	value
parameter	max_areas_per_map	5
parameter	max_areas_per_pathway_db	5
map	https://pdmap.uni.lu/minerva/api/	
map	https://progeria.uni.lu/minerva/api/	
pathway_db	WikiPathways_2019_Human	
pathway_db	Panther_2016	
\ No newline at end of file

parameters.sh

@@ -4,7 +4,12 @@ ORPHANET_IDS="130"
 
 DISGENET_CNT_THRESHOLD=50
 DISGENET_ASSOCIATION_SCORE_THRESHOLD="0"
+
 OPENTARGETS_CNT_THRESHOLD=50
 OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD="0.3"
+
+ENRICH_MAX_AREAS_PER_MAP=1
+MAX_AREAS_PER_PATHWAY_DB=1
+
 BUILD_MAP_GENERATOR=0 #1 for building it
 STOP_AFTER_STAGE=-1
\ No newline at end of file