Commit 240ebaae authored by David Hoksza's avatar David Hoksza
Browse files

ability to pass parameters to enrichment analysis from the parameters script

parent d41983b9
......@@ -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"
......
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
......@@ -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
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