removed smartmatch warning vep

GC-HBOC · Feb 22, 2024 · f05555f · f05555f
1 parent 5b83fd3
commit f05555f
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/src/annotation_service/annotation_jobs/vep_job.py b/src/annotation_service/annotation_jobs/vep_job.py
@@ -18,6 +18,7 @@ def __init__(self, job_config, refseq=False):
             self.job_name = "vep ensembl"
         self.refseq=refseq
         self.job_config = job_config
+        self.err_subber = re.compile(r"Smartmatch is experimental at /.*/VEP/AnnotationSource/File.pm line 472.")
 
 
     def execute(self, inpath, annotated_inpath, **kwargs):
@@ -33,7 +34,8 @@ def execute(self, inpath, annotated_inpath, **kwargs):
             vep_code, vep_stderr, vep_stdout = self._annotate_vep(inpath, annotated_inpath)
 
         ## stupid workaround for this specific vep warning:
-        if vep_stderr == "VEP runtime WARNING: Smartmatch is experimental at /mnt/storage2/users/ahdoebm1/HerediVar/tools/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472.":
+        vep_stderr = re.sub(self.err_subber, "", vep_stderr)
+        if vep_stderr.strip() == "VEP runtime WARNING:" or vep_stderr.strip() == "VEP runtime ERROR:":
             vep_stderr = ""
 
         self.handle_result(inpath, annotated_inpath, vep_code)