Merge branch 'production_ready' into 'master'

PDBE-4249: Offset for PRO ids in seq conservation call

See merge request pdbe-kb/services/pdbe-graph-api!400

app/uniprot.py

@@ -2600,6 +2600,9 @@ def get_sequence_conservation_uniprot_api(uniprot_accession):
         }
     }
 
+    first_residue = None
+    residue_id = None
+
     for score in result:
 
         scores_tuple = [
@@ -2625,9 +2628,19 @@ def get_sequence_conservation_uniprot_api(uniprot_accession):
             ('Y', score['hr.P_SCORE_Y'])
         ]
 
+        residue_id = score['residue_id']
+
+        # find the first residue
+        if not first_residue:
+            first_residue = residue_id
+
+        # PDBE-4249 - Offset for processed proteins
+        if uniprot_accession.startswith("PRO_"):
+            residue_id = residue_id - first_residue + 1
+
         residue_fragment = {
-            "start": score['residue_id'],
-            "end": score['residue_id'],
+            "start": residue_id,
+            "end": residue_id,
             "conservation_score": int(score['hr.CONSERVED_SCORE']),
             "tooltipContent": f"Conservation score: {score['hr.CONSERVED_SCORE']}",
             "amino": [],
@@ -2638,11 +2651,11 @@ def get_sequence_conservation_uniprot_api(uniprot_accession):
             (aa_code, p_score) = element
 
             residue_fragment["amino"].append({
-                "end": score['residue_id'],
+                "end": residue_id,
                 "oneLetterCode": aa_code,
                 "threeLetterCode": util_common.get_amino_one_to_three(aa_code),
                 "probability": float(p_score),
-                "start": score['residue_id'],
+                "start": residue_id,
                 "color": seq_conservation_aa_colors[aa_code],
                 "tooltipContent": f"Amino acid: {amino_acid_codes_one_to_three[aa_code]}<br/>Probability: {float(p_score) * 100:.2f}%"
             })