0-based positions

src/uta/loading.py

@@ -7,7 +7,7 @@
 import itertools
 import logging
 import time
-from typing import Any
+from typing import Any, Dict, List
 
 from biocommons.seqrepo import SeqRepo
 from bioutils.coordinates import strand_pm_to_int, MINUS_STRAND
@@ -685,32 +685,13 @@ def _fetch_origin_by_name(name):
             if ti.transl_except:
                 # if transl_except exists, it looks like this:
                 # (pos:333..335,aa:Sec);(pos:1017,aa:TERM)
-                for te in ti.transl_except.split(';'):
-                    # remove parens
-                    te = te.replace('(','').replace(')','')
-
-                    # extract positions
-                    pos_str, aa_str = te.split(',')
-                    pos_str = pos_str.removeprefix('pos:')
-                    if '..' in pos_str:
-                        start_position, _, end_position = pos_str.partition('..')
-                    else:
-                        start_position = end_position = pos_str
-
-                    # extract amino acid
-                    amino_acid = aa_str.removeprefix('aa:')
-
-                    u_te = usam.TranslationException(
-                        tx_ac=ti.ac,
-                        start_position=int(start_position),
-                        end_position=int(end_position),
-                        amino_acid=amino_acid,
-                    )
-                    session.add(u_te)
+                transl_except_list = ti.transl_except.split(';')
+                te_list = _create_translation_exceptions(transcript=ti.ac, transl_except_list=transl_except_list)
+                for te in te_list:
+                    session.add(usam.TranslationException(**te))
 
         if u_tx.gene_id != ti.gene_id:
-            raise Exception("{ti.ac}: GeneID changed from {u_tx.gene_id} to {ti.gene_id}".format(
-                u_tx=u_tx, ti=ti))
+            raise Exception("{ti.ac}: GeneID changed from {u_tx.gene_id} to {ti.gene_id}".format(u_tx=u_tx, ti=ti))
 
         # state: transcript now exists, either existing or freshly-created
 
@@ -736,6 +717,40 @@ def _fetch_origin_by_name(name):
                 p=(i_ti + 1) / n_rows * 100))
 
 
+def _create_translation_exceptions(transcript: str, transl_except_list: List[str]) -> List[Dict]:
+    """
+    Create TranslationException object data where start and end positions are 0-based, from transl_except data that is 1-based.
+    For example, [(pos:333..335,aa:Sec), (pos:1017,aa:TERM)] should result in start and end positions [(332, 335), (1016, 1017)]
+    """
+    result = []
+
+    for te in transl_except_list:
+        # remove parens
+        te = te.replace('(','').replace(')','')
+
+        # extract positions
+        pos_str, aa_str = te.split(',')
+        pos_str = pos_str.removeprefix('pos:')
+        if '..' in pos_str:
+            start_position, _, end_position = pos_str.partition('..')
+        else:
+            start_position = end_position = pos_str
+
+        # extract amino acid
+        amino_acid = aa_str.removeprefix('aa:')
+
+        result.append(
+            {
+                'tx_ac': transcript,
+                'start_position': int(start_position) - 1,
+                'end_position': int(end_position),
+                'amino_acid': amino_acid,
+            }
+        )
+
+    return result
+
+
 def refresh_matviews(session, opts, cf):
     session.execute(text("set role {admin_role};".format(
         admin_role=cf.get("uta", "admin_role"))))

tests/test_uta_loading.py

@@ -202,8 +202,28 @@ def test_load_txinfo(self):
             },
             {
                 'tx_ac': 'NM_080430.4',
-                'start_position': 205,
+                'start_position': 204,
                 'end_position': 207,
                 'amino_acid': 'Sec',
             },
         )
+
+
+class TestUtaLoadingFunctions(unittest.TestCase):
+    def test__create_translation_exceptions(self):
+        transl_except_list = ['(pos:333..335,aa:Sec)', '(pos:1017,aa:TERM)']
+        translation_exceptions = ul._create_translation_exceptions(transcript='dummy_tx', transl_except_list=transl_except_list)
+        self.assertEqual(translation_exceptions, [
+            {
+                'tx_ac': 'dummy_tx',
+                'start_position': 332,
+                'end_position': 335,
+                'amino_acid': 'Sec',
+            },
+            {
+                'tx_ac': 'dummy_tx',
+                'start_position': 1016,
+                'end_position': 1017,
+                'amino_acid': 'TERM',
+            },
+        ])