enable passing parameters file; fixing minerva variants

assemble.sh

 #!/usr/bin/env bash
 
+# Load parameters either from parameters.sh, or from a file provided as the first parameter of the script
+if [[ $1 == "" ]]; then
+    source parameters.sh
+else
+    source $1
+fi
 # ------------------------- PARAMETERS TO SET -------------------------
-source parameters.sh
+
+
 # ------------------------- PARAMETERS TO SET -------------------------
 
 ASSOCIATIONS_DIR=associations/

associations/minerva_variants.py

@@ -4,6 +4,7 @@ import json
 import argparse
 from typing import List, Dict, Set
 import requests
+import copy
 
 
 def get_dbsnp(ids: List[str]) -> List[Dict]:
@@ -119,7 +120,7 @@ def get_dbsnp(ids: List[str]) -> List[Dict]:
                         "position": position,
                         "original_dna": original_dna,
                         "alternative_dna": alternative_dna,
-                        "name": name,
+                        "gene_name": name,
                         "description": description,
                         "color": color,
                         "contig": contig,
@@ -158,13 +159,18 @@ def get_minerva_format(db_snps: List[Dict]) -> str:
     if len(db_snps) == 0:
         return out
 
+
     out += "#NAME=DISEASE_ASSOCIATED_VARIANTS\n"
     out += "#TYPE=GENETIC_VARIANT\n"
     out += "#GENOME_TYPE=UCSC\n"
     out += "#GENOME_VERSION=hg19\n"
-    out += "\t".join(db_snps[0].keys()) + "\n"
+    keys = list(db_snps[0].keys())
+    keys.remove('variant_identifier')
+    out += "\t".join(keys) + "\n"
     for snp in db_snps:
-        out += "\t".join(snp.values()) + "\n"
+        snp_cp = copy.deepcopy(snp)
+        del snp_cp['variant_identifier']
+        out += "\t".join(snp_cp.values()) + "\n"
 
     return out
 

parameters.sh

@@ -12,8 +12,8 @@ USE_OPENTARGETS=1
 OPENTARGETS_CNT_THRESHOLD=50
 OPENTARGETS_ASSOCIATION_SCORE_THRESHOLD="0.3"
 
-ENRICH_MAX_AREAS_PER_MAP=1
-MAX_AREAS_PER_PATHWAY_DB=1
+ENRICH_MAX_AREAS_PER_MAP=5
+MAX_AREAS_PER_PATHWAY_DB=5
 
 BUILD_MAP_GENERATOR=0 #1 for building it
 STOP_AFTER_STAGE=-1
\ No newline at end of file