From d211eacb74522bc54468f191a2ec962eba894682 Mon Sep 17 00:00:00 2001
From: MarvinDo <qarst@gmx.de>
Date: Fri, 23 Feb 2024 11:29:14 +0100
Subject: [PATCH] bugfix

---
 .../annotation_jobs/heredicare_job.py         |  3 +-
 .../annotation_jobs/spliceai_job.py           | 29 +++++--------------
 .../webapp/templates/index.html               |  1 +
 3 files changed, 9 insertions(+), 24 deletions(-)

diff --git a/src/annotation_service/annotation_jobs/heredicare_job.py b/src/annotation_service/annotation_jobs/heredicare_job.py
index 0c605de0..87a406d5 100644
--- a/src/annotation_service/annotation_jobs/heredicare_job.py
+++ b/src/annotation_service/annotation_jobs/heredicare_job.py
@@ -61,7 +61,7 @@ def save_to_db(self, info, variant_id, conn):
                 err_msg += "There was an error during variant retrieval from heredicare: " + str(message)
                 status_code = 1
             else:
-                print(heredicare_variant)
+                #print(heredicare_variant)
                 n_fam = heredicare_variant["N_FAM"]
                 n_pat = heredicare_variant["N_PAT"]
                 consensus_class = heredicare_variant["PATH_TF"] if heredicare_variant["PATH_TF"] != "-1" else None
@@ -86,7 +86,6 @@ def save_to_db(self, info, variant_id, conn):
                 for key in heredicare_variant:
                     if key.startswith("PATH_Z") and heredicare_variant[key] is not None:
                         zid = int(key[6:])
-                        print(zid)
                         classification = heredicare_variant[key] if heredicare_variant[key] != "-1" else None
                         conn.insert_heredicare_center_classification(heredicare_annotation_id, zid, classification, comment = None) # TODO! COMMENT!
 
diff --git a/src/annotation_service/annotation_jobs/spliceai_job.py b/src/annotation_service/annotation_jobs/spliceai_job.py
index 1b0fc154..09ac086d 100644
--- a/src/annotation_service/annotation_jobs/spliceai_job.py
+++ b/src/annotation_service/annotation_jobs/spliceai_job.py
@@ -22,18 +22,19 @@ def execute(self, inpath, annotated_inpath, **kwargs):
 
         self.print_executing()
 
-
         spliceai_code, spliceai_stderr, splicai_stdout = self.annotate_missing_spliceai(inpath, annotated_inpath)
 
-
         self.handle_result(inpath, annotated_inpath, spliceai_code)
+
         return spliceai_code, spliceai_stderr, splicai_stdout
 
 
     def save_to_db(self, info, variant_id, conn):
-        for prefix in ['snv', 'indel']:
-            self.insert_annotation(variant_id, info, prefix + '_SpliceAI=', 7, conn, value_modifier_function= lambda value : ','.join(['|'.join(x.split('|')[1:]) for x in value.replace(',', '&').split('&')]) )
-            self.insert_annotation(variant_id, info, prefix + '_SpliceAI=', 8, conn, value_modifier_function= lambda value : ','.join([str(max([float(x) for x in x.split('|')[2:6]])) for x in value.replace(',', '&').split('&')]) )
+        recent_annotation_ids = conn.get_recent_annotation_type_ids()
+
+        for prefix in ['snv_', 'indel_', '']:
+            self.insert_annotation(variant_id, info, prefix + 'SpliceAI=', recent_annotation_ids["spliceai_details"], conn, value_modifier_function= lambda value : ','.join(['|'.join(x.split('|')[1:]) for x in value.replace(',', '&').split('&')]) )
+            self.insert_annotation(variant_id, info, prefix + 'SpliceAI=', recent_annotation_ids["spliceai_max_delta"], conn, value_modifier_function= lambda value : ','.join([str(max([float(x) for x in x.split('|')[2:6]])) for x in value.replace(',', '&').split('&')]) )
         
         return 0, ""
 
@@ -41,9 +42,6 @@ def save_to_db(self, info, variant_id, conn):
 
 
     def annotate_missing_spliceai(self, input_vcf_path, output_vcf_path):
-        #input_file = open(input_vcf_path, 'r')
-        #temp_path = tempfile.gettempdir() + '/' + str(uuid.uuid4()) + '.vcf'
-        #temp_file = open(temp_path, 'w')
 
         found_spliceai_header = False
         need_annotation = False
@@ -54,7 +52,6 @@ def annotate_missing_spliceai(self, input_vcf_path, output_vcf_path):
         with open(input_vcf_path, 'r') as input_file:
             for line in input_file:
                 if line.startswith('#'):
-                    #temp_file.write(line)
                     if line.startswith('##INFO=<ID=snv_SpliceAI') or line.startswith('##INFO=<ID=indel_SpliceAI') :
                         found_spliceai_header = True
                     continue
@@ -63,19 +60,10 @@ def annotate_missing_spliceai(self, input_vcf_path, output_vcf_path):
                         continue
                     
                     need_annotation = True
-                    #temp_file.write(line)
-        #temp_file.close()
+
         if not found_spliceai_header:
             errors.append("SpliceAI WARNING: did not find a SpliceAI INFO entry in input vcf, did you annotate the file using a precomputed file before?")
         if need_annotation:
-            #returncode, stderr, stdout = functions.execute_command(['sed', '-i', '/SpliceAI/d', input_vcf_path], "sed")
-            #if returncode != 0:
-            #    errors.append(stderr)
-            #returncode, stderr, stdout = functions.execute_command(['chmod', '777', input_vcf_path], 'chmod')
-            #if returncode != 0:
-            #    errors.append(stderr)
-            #returncode, stderr, stdout = functions.execute_command(["ls", "-l", "/tmp"], "ls")
-            #print(stdout)
             spliceai_code, spliceai_stderr, spliceai_stdout = self.annotate_spliceai_algorithm(input_vcf_path, output_vcf_path)
             if 'SpliceAI runtime ERROR:' in spliceai_stderr:
                 errors.append(spliceai_stderr)
@@ -84,7 +72,6 @@ def annotate_missing_spliceai(self, input_vcf_path, output_vcf_path):
 
         # need to insert some code here to merge the newly annotated variants and previously 
         # annotated ones from the db if there are files which contain more than one variant! 
-        #input_file.close()
 
 
 
@@ -116,5 +103,3 @@ def annotate_spliceai_algorithm(self, input_vcf_path, output_vcf_path):
 
 
 
-
-
diff --git a/src/frontend_celery/webapp/templates/index.html b/src/frontend_celery/webapp/templates/index.html
index 440c876b..ea8f01b1 100644
--- a/src/frontend_celery/webapp/templates/index.html
+++ b/src/frontend_celery/webapp/templates/index.html
@@ -106,6 +106,7 @@ <h4>Changelog</h4>
             <li>A selected criterium would automatically uncheck if a mutually exclusive criterium was unselected and the mutually exclusive criterium itself is mutually exclusive with the selected criterium</li>
             <li>Fixed default strength for supporting criteria in ACMG standard scheme</li>
             <li>Fixed wrapping of PVS1_mod criterium</li>
+            <li>Fixed a bug where the SpliceAI scores would not show on longer indels</li>
         </ul>
     </div>
     <div class="underline">v 1.8 (21.02.2024)</div>