added timestamps to logging

assemble.sh

@@ -35,50 +35,62 @@ check_exit_code(){
     fi
 }
 
+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
-echo "Disgenet gene and variant associations stored in ${disgenet_out_path}"
+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
-echo "Opentargets gene and variant associations stored in ${opentargets_out_path}"
+log "Opentargets gene and variant associations stored in ${opentargets_out_path}"
 
 # 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}
 check_exit_code
-echo "Integration with ClinVar stored in ${genes_variants_out_path}"
+log "Integration with ClinVar stored in ${genes_variants_out_path}"
 
 genes_line=`cat ${genes_variants_out_path} | grep "genes in total"`
 genes_out_path=${genes_variants_out_path/02-genes_variants/03-genes}
 #echo ${genes_line#*:} | sed 's/\,/\n/g' > ${genes_out_path}
 echo ${genes_line#*:} | tr ',' '\n' > ${genes_out_path}
-echo "Genes stored in ${genes_out_path}"
+log "Genes stored in ${genes_out_path}"
 
-echo "Extending genes list"
+log "Extending genes list..."
 text_mining_out_path=${genes_out_path/03-genes/03-text-mining}
 echo Rscript --vanilla ${EXTEND_DIR}/get_extended_network.R ${genes_out_path} ${EXTEND_CONFIG}
 check_exit_code
 cp ${EXTEND_DIR}/output.txt ${text_mining_out_path}
-echo "Genes list extended"
+log "Genes list extended"
+
+
 
 minerva_genes_out_path=${RES_DIR}/04-minerva-genes.txt
 $PYTHON_BIN $ASSOCIATIONS_DIR/minerva_genes.py -f ${genes_out_path} > ${minerva_genes_out_path}
 check_exit_code
+log "Genes stored in ${minerva_genes_out_path}"
+
 
 var_line=`cat ${genes_variants_out_path} | grep "variants in total"`
 variants_out_path=${genes_variants_out_path/02-genes_variants/03-variants}
 #echo ${var_line#*:} | sed 's/\,/\n/g' > ${variants_out_path}
 echo ${var_line#*:} | tr ',' '\n' > ${variants_out_path}
-echo "Variants stored in ${variants_out_path}"
+log "Variants stored in ${variants_out_path}"
 
+log "Getting detailed variants information..."
 minerva_variants_out_path=${RES_DIR}/04-minerva-variants.txt
 $PYTHON_BIN $ASSOCIATIONS_DIR/minerva_variants.py -f ${variants_out_path} > ${minerva_variants_out_path}
+log "Detailed variants information obtained"
 check_exit_code
 
 if [ ${STOP_AFTER_STAGE} = 1 ]; then
@@ -86,7 +98,7 @@ if [ ${STOP_AFTER_STAGE} = 1 ]; then
     exit 0
 fi
 # ------------------------------ 2. Obtain pathways ------------------------------
-echo "Retrieving enriched pathways"
+log "Retrieving enriched pathways..."
 
 tr '\r' '\n' < ${ENRICHMENT_CONFIG} > ${ENRICHMENT_CONFIG_TMP}
 
@@ -104,7 +116,7 @@ mv enriched_pathways.txt ${enriched_paths_out_path}
 
 rm ${ENRICHMENT_CONFIG_TMP}
 
-echo "Enriched pathways obtained"
+log "Enriched pathways retrieved"
 
 
 if [ ${STOP_AFTER_STAGE} = 2 ]; then
@@ -118,16 +130,16 @@ if [ ${BUILD_MAP_GENERATOR} = 1 ]; then
     mvn -DskipTests=true clean install -pl biohackathon -am
     cd ..
 fi
-echo "Map generator built"
-echo "Assembling the map from pathways ..."
+log "Map generator built"
+log "Assembling the map from pathways ..."
 map_out_path=${RES_DIR}/06-minerva_map.xml
 java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file  ${enriched_maps_out_path} --text-mining-file  ${text_mining_out_path} --output-file ${map_out_path}
 #java -Xmx4g -jar ${MAP_GENERATOR_DIR}/biohackathon/target/biohackathon-1.0-jar-with-dependencies.jar --enrichr-file ${enriched_paths_out_path} --minerva-file  ${enriched_maps_out_path} --output-file ${map_out_path}
 check_exit_code
 
-echo "Pathwaygs assembled into ${map_out_path}"
+log "Pathwaygs assembled into ${map_out_path}"
 
-echo "Combining map with overlays"
+log "Combining the map with overlays"
 
 tmp_dir=${RES_DIR}/tmp/
 tmp_dir_layouts=${tmp_dir}/layouts/
@@ -147,4 +159,4 @@ cd -
 mv ${tmp_dir}/tmp.zip ${map_zip_out_path}
 
 rm -rf ${tmp_dir}
-echo "Final map with overlays stored in ${map_zip_out_path}"
\ No newline at end of file
+log "Final map with overlays stored in ${map_zip_out_path}"
\ No newline at end of file