From f55c02dd1b321ce1fc3a1aa931ab0914206c8209 Mon Sep 17 00:00:00 2001
From: MarvinDo <qarst@gmx.de>
Date: Mon, 3 Jun 2024 15:56:22 +0200
Subject: [PATCH] fixed a bug in consequence job when a variant would not
 recieve any consequences

---
 .../annotation_jobs/consequence_job.py           | 16 ++++++++++++++++
 src/annotation_service/main.py                   |  2 +-
 src/common/functions.py                          |  1 -
 3 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/annotation_service/annotation_jobs/consequence_job.py b/src/annotation_service/annotation_jobs/consequence_job.py
index 00b7f39a..79c1bbe7 100644
--- a/src/annotation_service/annotation_jobs/consequence_job.py
+++ b/src/annotation_service/annotation_jobs/consequence_job.py
@@ -98,12 +98,28 @@ def annotate_consequence(self, input_vcf, output_vcf):
             functions.rm(tmp_vcf)
             return returncode, err_msg, vcf_errors
         
+
+        with open(tmp_vcf, "r") as tmp_file:
+            tmp_text = tmp_file.read()
+            new_annotation = functions.find_between(tmp_text, "CSQ_ensembl=", '(;|$)')
+            if new_annotation is not None and new_annotation == '':
+                functions.rm(tmp_vcf)
+                os.rename(input_vcf, tmp_vcf)
+        
         # annotate refseq consequences
         command = [os.path.join(paths.ngs_bits_path, "VcfAnnotateConsequence")]
         command.extend([ "-gff", paths.refseq_transcript_4_consequence_path, "-ref", paths.ref_genome_path, "-all",  "-tag", "CSQ_refseq", "-in", tmp_vcf, "-out", output_vcf])
         returncode, err_msg, vcf_errors = functions.execute_command(command, 'VcfAnnotateConsequenceRefSeq')
 
+        with open(output_vcf, "r") as tmp_file:
+            tmp_text = tmp_file.read()
+            new_annotation = functions.find_between(tmp_text, "CSQ_refseq=", '(;|$)')
+            if new_annotation is not None and new_annotation == '':
+                functions.rm(output_vcf)
+                os.rename(tmp_vcf, output_vcf)
+        
         functions.rm(tmp_vcf)
+
         return returncode, err_msg, vcf_errors
 
 
diff --git a/src/annotation_service/main.py b/src/annotation_service/main.py
index 13e5876c..d96df730 100644
--- a/src/annotation_service/main.py
+++ b/src/annotation_service/main.py
@@ -29,7 +29,7 @@ def get_default_job_config():
 
         # consequences
         'do_consequence': True,
-        'do_vep': True,
+        'do_vep': False,
 
         #vcf annotate from vcf
         'do_dbsnp': True,
diff --git a/src/common/functions.py b/src/common/functions.py
index 73a9ac38..96296743 100644
--- a/src/common/functions.py
+++ b/src/common/functions.py
@@ -669,7 +669,6 @@ def rm(path):
     if os.path.exists(path): 
         os.remove(path)
 
-
 def remove_oldest_file(folder, maxfiles=10):
     if os.path.exists(folder):
         list_of_files = os.listdir(folder)