fixed a bug

GC-HBOC · Nov 8, 2023 · b49231b · b49231b
1 parent 8c59e43
commit b49231b
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/src/common/db_IO.py b/src/common/db_IO.py
@@ -2756,7 +2756,7 @@ def get_transcripts_from_names(self, transcript_names, remove_unknown = False):
         transcripts = [self.convert_raw_transcript(transcript_raw) for transcript_raw in transcripts_raw]
 
         if not remove_unknown:
-            transcripts_not_in_db = list(set(transcript_names) - set([x[2] for x in transcripts_raw]))
+            transcripts_not_in_db = list(set(transcript_names) - set([x[3] for x in transcripts_raw]))
             transcripts_not_in_db = [models.Transcript(id=None, gene=None, name=transcript_name, biotype=None, length=None, chrom="", start=0, end=0, orientation="", source="ensembl" if transcript_name.startswith('ENST') else "refseq", is_gencode_basic=None,is_mane_select=None,is_mane_plus_clinical=None,is_ensembl_canonical=None) for transcript_name in transcripts_not_in_db]
             transcripts.extend(transcripts_not_in_db)
 

diff --git a/src/common/functions.py b/src/common/functions.py
@@ -683,7 +683,7 @@ def sort_transcript_dict(input_dict):
 def sort_transcripts(transcript_names):
     from common.db_IO import Connection
     conn = Connection()
-    transcripts = conn.get_transcripts_from_names(transcript_names)
+    transcripts = conn.get_transcripts_from_names(transcript_names, remove_unknown = True)
     #print(transcripts)
     conn.close()
     transcripts_sorted = order_transcripts(transcripts)

diff --git a/src/common/models.py b/src/common/models.py
@@ -872,14 +872,22 @@ def get_preferred_transcripts(self):
 
         if consequences is None:
             return None
-        if len(consequences) == 0:
-            return None
 
         sortable_dict = {}
         for consequence in consequences:
             if consequence.transcript.source == 'ensembl':
                 sortable_dict[consequence.transcript.name] = consequence
+
+        if len(sortable_dict) == 0:
+            return None
+
+        #print("sortable dict:")
+        #print(sortable_dict)
         transcripts_sorted, consequences_sorted = functions.sort_transcript_dict(sortable_dict)
+        #print("transcripts_sorted:")
+        #print(transcripts_sorted)
+        #print("consequences_sorted:")
+        #print(consequences_sorted)
         result.append(consequences_sorted.pop(0)) # always append the first one
         for consequence in consequences_sorted: # scan for all mane select transcripts
             if consequence.transcript.is_mane_select: