From 55f23472432a90f758a1c58d3c296a1ae0595612 Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshmt.ac.uk>
Date: Tue, 12 Mar 2019 17:45:47 +0000
Subject: [PATCH] update variants schema

---
 pathogenprofiler/barcode.py  | 13 ++++---------
 pathogenprofiler/profiler.py |  8 +++++---
 2 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/pathogenprofiler/barcode.py b/pathogenprofiler/barcode.py
index 7e763ab..6459264 100644
--- a/pathogenprofiler/barcode.py
+++ b/pathogenprofiler/barcode.py
@@ -51,7 +51,7 @@ def barcode(mutations,barcode_bed):
 		final_results.append(tmp)
 	return final_results
 
-def db_compare(mutations,db_file,bed_file,deletions=None):
+def db_compare(mutations,db_file):
 	db = json.load(open(db_file))
 	annotated_mutations = mutations
 	for i in range(len(mutations["variants"])):
@@ -69,17 +69,12 @@ def db_compare(mutations,db_file,bed_file,deletions=None):
 				db_var_match = db[var["gene_id"]]["any_indel_nucleotide_%s" % get_indel_nucleotide(var["change"])]
 			elif "stop_gained" in var["type"] and "premature_stop" in db[var["gene_id"]]:
 				db_var_match = db[var["gene_id"]]["premature_stop"]
+			elif "large_deletion" in var["type"] and "large_deletion" in db[var["gene_id"]]:
+				db_var_match = db[var["gene_id"]]["large_deletion"]
 			if db_var_match:
 				if "annotation" not in annotated_mutations["variants"][i]:
 					annotated_mutations["variants"][i]["annotation"] = {}
 				for key in db_var_match:
 					annotated_mutations["variants"][i]["annotation"][key] = db_var_match[key]
-	if deletions:
-		bed = load_bed(bed_file,[1,2,3,4,5,6],4)
-		for deletion in deletions:
-			tmp = {"genome_pos":deletion["start"],"gene_id":deletion["region"],"chr":deletion["chr"],"freq":1,"type":"large_deletion","change":"%(chr)s:g.%(start)s_%(end)sdel" % deletion}
-			if deletion["region"] in db and "large_deletion" in db[deletion["region"]]:
-				tmp["annotation"] =  db[deletion["region"]]["large_deletion"]			
-			mutations["variants"].append(tmp)
-	#1883443: {u'C': 0.8, u'A': 0.2}
+	
 	return annotated_mutations
diff --git a/pathogenprofiler/profiler.py b/pathogenprofiler/profiler.py
index c094f4c..e7fb2e8 100644
--- a/pathogenprofiler/profiler.py
+++ b/pathogenprofiler/profiler.py
@@ -43,8 +43,10 @@ def profiler(conf_file,prefix,r1=None,r2=None,bam_file=None,call_method="low",mi
 		if run_delly:
 			delly_bcf = bam_obj.run_delly()
 			deletions = delly_bcf.overlap_bed(conf["bed"])
-			results = db_compare(db_file=conf["json_db"],mutations=results,bed_file=conf["bed"],deletions=deletions)
-		else:
-			results = db_compare(db_file=conf["json_db"],mutations=results,bed_file=conf["bed"])
+			for deletion in deletions:
+				tmp = {"genome_pos":deletion["start"],"gene_id":deletion["region"],"chr":deletion["chr"],"freq":1,"type":"large_deletion","change":"%(chr)s_%(start)s_%(end)s" % deletion}
+				results["variants"].append(tmp)
+
+		results = db_compare(db_file=conf["json_db"],mutations=results)
 
 		return results