Fixed EnsemblTRs not being shown

acg-team · Mar 7, 2023 · fdcc6a3 · fdcc6a3
1 parent 1e2ab08
commit fdcc6a3
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 5 deletions.
diff --git a/strAPI/genes.py b/strAPI/genes.py
@@ -15,6 +15,7 @@ def get_exons_by_transcript(db, cds_only, transcript_obj):
         return list(sorted(exons, key=lambda x : x.start, reverse=True))
 
 def get_gene_info(db, gene_names, ensembl_ids, reqion_query):
+    genes = []
     if gene_names:
         genes = db.query(Gene).filter(Gene.name.in_(gene_names)).all()
     elif ensembl_ids:

diff --git a/strAPI/main.py b/strAPI/main.py
@@ -203,7 +203,11 @@ def repeats_to_list(repeats):
             print(r)
             repeat = r[0]
             gene = r[1]
-            crcvar = r[3]
+            if r[3]:
+                crcvar = dict(r[3])
+            else:
+                crcvar = dict(total_calls=None, frac_variable = None, avg_size_diff = None)
+
             rows.append({
                 "repeat_id": repeat.id,
                 "chr": repeat.chr,
@@ -217,9 +221,9 @@ def repeats_to_list(repeats):
                 "strand": gene.strand,
                 "gene_name": gene.name,
                 "gene_desc": gene.description,
-                "total_calls": crcvar.total_calls,
-                "frac_variable": crcvar.frac_variable,
-                "avg_size_diff": crcvar.avg_size_diff
+                "total_calls": crcvar["total_calls"],
+                "frac_variable": crcvar["frac_variable"],
+                "avg_size_diff": crcvar["avg_size_diff"]
             })
         return rows
 
@@ -245,7 +249,7 @@ def repeats_to_csv(repeats):
             ).join(models.Gene).where(models.Gene.id == models.GenesRepeatsLink.gene_id  #INNER JOIN genes ON genes.id = genes_repeats.gene_id)
             ).join(models.Repeat).where(models.Repeat.id == models.GenesRepeatsLink.repeat_id #INNER JOIN repeats on repeats.id = genes_repeats.repeat_id)
             ).filter(models.Gene.id.in_(gene_obj_ids)
-            ).join(models.CRCVariation).where(models.Repeat.id == models.CRCVariation.repeat_id  
+            ).join(models.CRCVariation, isouter=True 
             ).order_by(nullslast(models.CRCVariation.frac_variable.desc())).order_by(models.CRCVariation.total_calls)
 
         repeats = db.exec(statement)