enrichment integrated in the pipeline. updated readme

README.md

@@ -7,6 +7,30 @@ Code and comments to [https://r3.pages.uni.lu/biocuration/resources/biohackathon
 - Python 3.x
 - R
 
+If the pipeline is run at clean Linux installation you might need to install the following libraries 
+(`sudo apt-get install` on Ubuntu) prior to running the code:
+- libcurl
+- libssl-dev
+- libxml2-dev
+
+### Execution
+
+To execute the pipeline, set the values of parameters in the `PARAMETERS TO SET` 
+section of the `assamble.sh` script file. The main parameter here is the list of
+[Orphanet](https://www.orpha.net/consor/cgi-bin/index.php?lng=EN) disease numbers.
+When the parameters are set, run the pipeline:
+
+```
+bash assemble.sh 
+```
+
+This will run the pipeline described in the next section and eventually output a
+ZIP file with a map which can then be imported in [MINERVA](https://minerva.pages.uni.lu/doc/)
+as a disease maps integrating all the found enriched pathways together with
+genetic an variant [overlays](https://minerva.pages.uni.lu/doc/user_manual/v14.0/index/#overlays-tab).
+
 ### Pipeline
 
-- [Retrieval of gene-disease mappging and variants](associations/README.md).
\ No newline at end of file
+
+1. [Retrieval of gene-disease mappging and variants](associations/README.md).
+2. [Enrichment]()
\ No newline at end of file

assamble.sh → assemble.sh

 #!/usr/bin/env bash
 
+# ------------------------- PARAMETERS TO SET -------------------------
+ORPHANET_IDS="130"
+DISGENET_CNT_THRESHOLD=50
+# ------------------------- PARAMETERS TO SET -------------------------
+
 ASSOCIATIONS_DIR=associations/
 ASSOCIATIONS_DATA_DIR=$ASSOCIATIONS_DIR/data/
 RES_DIR=results
+ENRICHMENT_DIR=enrichment/
+ENRICHMENT_CONFIG=${ENRICHMENT_DIR}/config.txt
 PYTHON_BIN=python3
 
-ORPHANET_IDS="130"
 #ORPHANET_IDS="33,67046,79327,79321,86309"
 ORPHANET_IDS_UNDERSCORE=${ORPHANET_IDS//,/_}
-DISGENET_CNT_THRESHOLD=50
 
 mkdir $RES_DIR
 
@@ -23,7 +28,7 @@ echo "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#*:} > ${genes_out_path}
+echo ${genes_line#*:} | sed 's/\,/\n/g' > ${genes_out_path}
 echo "Genes stored in ${genes_out_path}"
 
 minerva_genes_out_path=${RES_DIR}/04-minerva-genes-id_${ORPHANET_IDS_UNDERSCORE}.txt
@@ -31,13 +36,17 @@ $PYTHON_BIN $ASSOCIATIONS_DIR/minerva_genes.py -f ${genes_out_path} > ${minerva_
 
 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#*:} > ${variants_out_path}
+echo ${var_line#*:} | sed 's/\,/\n/g' > ${variants_out_path}
 echo "Variants stored in ${variants_out_path}"
 
 minerva_variants_out_path=${RES_DIR}/04-minerva-variants-id_${ORPHANET_IDS_UNDERSCORE}.txt
 $PYTHON_BIN $ASSOCIATIONS_DIR/minerva_variants.py -f ${variants_out_path} > ${minerva_variants_out_path}
 
 # ------------------------------ 2. Obtain pathways ------------------------------
-#R -f path_to_script
+echo "Rscript --vanilla enrichment/enrich_maps.R enrich_maps.R ${genes_out_path} ${ENRICHMENT_CONFIG}"
+enriched_maps_out_path=$RES_DIR/05-enriched_disease_maps.txt
+enriched_paths_out_path=$RES_DIR/05-enriched_pathways.txt
+cp enriched_disease_maps.txt ${enriched_maps_out_path}
+cp enriched_pathways.txt ${enriched_paths_out_path}
 
 

associations/minerva_genes.py

@@ -29,4 +29,4 @@ if __name__ == '__main__':
     with open(args.file) as f:
         gene_symbols = f.read()
 
-        print(get_minerva_format(gene_symbols.strip().split(",")))
+        print(get_minerva_format(gene_symbols.strip().split("\n")))

associations/minerva_variants.py

@@ -168,5 +168,5 @@ if __name__ == '__main__':
 
     with open(args.file) as f:
         dbsnp_ids = f.read()
-        db_snps = get_dbsnp(dbsnp_ids.split(","))
+        db_snps = get_dbsnp(dbsnp_ids.split("\n"))
         print(get_minerva_format(remove_snps_with_multiple_uniprot_ids(db_snps)))