Merge pull request #230 from ga4gh/2-alpha-allele-translator

Updates for spdi and hgvs to/from

src/ga4gh/vrs/extras/translator.py

@@ -6,6 +6,7 @@
 """
 
 from collections.abc import Mapping
+from typing import Union
 import logging
 import re
 
@@ -87,7 +88,8 @@ def translate_to(self, vo, fmt):
 
 
     ############################################################################
-    ## INTERNAL
+    # INTERNAL
+
 
     def _from_beacon(self, beacon_expr, assembly_name=None):
         """Parse beacon expression into VRS Allele
@@ -324,7 +326,7 @@ def ir_stype(a):
         if not self.is_valid_allele(vo):
             raise ValueError("_to_hgvs requires a VRS Allele with SequenceLocation and LiteralSequenceExpression")
 
-        sequence = str(vo.location.sequence)
+        sequence = str(export_sequencelocation_sequence_id(vo.location.sequence))
         aliases = self.data_proxy.translate_sequence_identifier(sequence, namespace)
 
         # infer type of sequence based on accession
@@ -350,9 +352,10 @@ def ir_stype(a):
                 ref = self.data_proxy.get_sequence(sequence, start, end)
                 start += 1
             ival = hgvs.location.Interval(
-                start=hgvs.location.start,
-                end=hgvs.location.end)
-            alt = str(vo.state.sequence) or None  # "" => None
+                start=str(vo.location.start),
+                end=str(vo.location.end)
+            )
+            alt = str(vo.state.sequence.root) or None  # "" => None
             edit = hgvs.edit.NARefAlt(ref=ref, alt=alt)
 
         posedit = hgvs.posedit.PosEdit(pos=ival, edit=edit)
@@ -389,7 +392,6 @@ def ir_stype(a):
 
         return list(set(hgvs_exprs))
 
-
     def _to_spdi(self, vo, namespace="refseq"):
         """generates a *list* of SPDI expressions for VRS Allele.
 
@@ -411,11 +413,11 @@ def _to_spdi(self, vo, namespace="refseq"):
         if not self.is_valid_allele(vo):
             raise ValueError("_to_spdi requires a VRS Allele with SequenceLocation and LiteralSequenceExpression")
 
-        sequence = str(vo.location.sequence)
+        sequence = str(export_sequencelocation_sequence_id(vo.location.sequence))
         aliases = self.data_proxy.translate_sequence_identifier(sequence, namespace)
         aliases = [a.split(":")[1] for a in aliases]
         start, end = vo.location.start, vo.location.end
-        spdi_tail = f":{start}:{end-start}:{vo.state.sequence}"
+        spdi_tail = f":{start}:{end-start}:{vo.state.sequence.root}"
         spdis = [a + spdi_tail for a in aliases]
         return spdis
 
@@ -434,13 +436,13 @@ def _hgvs_parser(self):
 
 
     def _post_process_imported_allele(self, allele):
-        """Provide common post-processing for imported Alleles IN-PLACE.
-
+        """
+        Provide common post-processing for imported Alleles IN-PLACE.
         """
 
         if self.translate_sequence_identifiers:
             seq_id = self.data_proxy.translate_sequence_identifier(allele.location.sequence.root, "ga4gh")[0]
-            allele.location.sequence = seq_id
+            allele.location.sequence.root = seq_id
 
         if self.normalize:
             allele = normalize(allele, self.data_proxy)
@@ -469,10 +471,16 @@ def _seq_id_mapper(self, ir):
     to_translators = {
         "hgvs": _to_hgvs,
         "spdi": _to_spdi,
-        #"gnomad": to_gnomad,
+        # "gnomad": to_gnomad,
     }
 
 
+def export_sequencelocation_sequence_id(
+        location_sequence: Union[models.IRI, models.SequenceReference]):
+    if isinstance(location_sequence, models.IRI):
+        return location_sequence.root
+    elif isinstance(location_sequence, models.SequenceReference):
+        return location_sequence.refgetAccession
 
 
 if __name__ == "__main__":
@@ -504,8 +512,8 @@ def _seq_id_mapper(self, ir):
             },
             "type": "Allele"
         }, {
-           "end": 22,
-           "start": 21,
+            "end": 22,
+            "start": 21,
         }
     ]
     formats = ["hgvs", "gnomad", "beacon", "spdi", "vrs", None]

src/ga4gh/vrs/normalize.py

@@ -15,15 +15,28 @@
 _logger = logging.getLogger(__name__)
 
 
-def _normalize_allele(allele, data_proxy):
-    sequence = SequenceProxy(data_proxy, allele.location.sequence)
+def _normalize_allele(input_allele, data_proxy):
+    """
+    Converts .location.sequence into an IRI if it is a SequenceReference because it makes the code simpler.
+    If it started as a sequence reference, put it back as one at the end.
+    """
+    allele = pydantic_copy(input_allele)
+    sequence_reference = None
+    if isinstance(allele.location.sequence, models.SequenceReference):
+        sequence_reference = allele.location.sequence
+        allele.location.sequence = models.IRI(sequence_reference.refgetAccession)
+
+    sequence = SequenceProxy(data_proxy, allele.location.sequence.root)
 
     ival = (allele.location.start, allele.location.end)
 
     _allele_state = allele.state.type
     _states_with_sequence = ["ReferenceLengthExpression", "LiteralSequenceExpression"]
     if _allele_state in _states_with_sequence:
-        alleles = (None, allele.state.sequence)
+        alleles = (None, allele.state.sequence.root)
+    elif _allele_state == "RepeatedSequenceExpression" and \
+            allele.state.seq_expr.type in _states_with_sequence:
+        alleles = (None, allele.state.seq_expr.sequence.root)
     else:
         alleles = (None, "")
 
@@ -40,15 +53,22 @@ def _normalize_allele(allele, data_proxy):
         new_allele.location.end = new_ival[1]
 
         if new_allele.state.type in _states_with_sequence:
-            new_allele.state.sequence = new_alleles[1]
+            new_allele.state.sequence = models.SequenceString(new_alleles[1])
     except ValueError:
         # Occurs for ref agree Alleles (when alt = ref)
         pass
 
+    if sequence_reference:
+        new_allele.location.sequence = sequence_reference
+
     return new_allele
 
 
+# TODO _normalize_genotype?
+
+
 def _normalize_haplotype(o, data_proxy=None):
+
     o.members = sorted(o.members, key=ga4gh_digest)
     return o
 

tests/conftest.py

@@ -15,15 +15,18 @@ def dataproxy():
 
 @pytest.fixture(scope="session")
 def rest_dataproxy():
-    return SeqRepoRESTDataProxy(base_url="http://localhost:5000/seqrepo")
+    return SeqRepoRESTDataProxy(
+        base_url=os.environ.get(
+            "SEQREPO_REST_URL",
+            "http://localhost:5000/seqrepo"))
 
 
 @pytest.fixture(scope="session")
 def tlr(rest_dataproxy):
     return Translator(
         data_proxy=rest_dataproxy,
         default_assembly_name="GRCh38",
-    # TODO: Set these to defaults and adjust relevant tests
+        # TODO: Set these to defaults and adjust relevant tests
         identify=False,
         normalize=False,
         translate_sequence_identifiers=True,

tests/extras/cassettes/test_to_spdi.yaml

@@ -9,7 +9,49 @@ interactions:
       Connection:
       - keep-alive
       User-Agent:
-      - python-requests/2.28.1
+      - python-requests/2.31.0
+    method: GET
+    uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000013.11
+  response:
+    body:
+      string: "{\n  \"added\": \"2016-08-27T23:50:14Z\",\n  \"aliases\": [\n    \"GRCh38:13\",\n
+        \   \"GRCh38:chr13\",\n    \"GRCh38.p1:13\",\n    \"GRCh38.p1:chr13\",\n    \"GRCh38.p10:13\",\n
+        \   \"GRCh38.p10:chr13\",\n    \"GRCh38.p11:13\",\n    \"GRCh38.p11:chr13\",\n
+        \   \"GRCh38.p12:13\",\n    \"GRCh38.p12:chr13\",\n    \"GRCh38.p2:13\",\n
+        \   \"GRCh38.p2:chr13\",\n    \"GRCh38.p3:13\",\n    \"GRCh38.p3:chr13\",\n
+        \   \"GRCh38.p4:13\",\n    \"GRCh38.p4:chr13\",\n    \"GRCh38.p5:13\",\n    \"GRCh38.p5:chr13\",\n
+        \   \"GRCh38.p6:13\",\n    \"GRCh38.p6:chr13\",\n    \"GRCh38.p7:13\",\n    \"GRCh38.p7:chr13\",\n
+        \   \"GRCh38.p8:13\",\n    \"GRCh38.p8:chr13\",\n    \"GRCh38.p9:13\",\n    \"GRCh38.p9:chr13\",\n
+        \   \"MD5:a5437debe2ef9c9ef8f3ea2874ae1d82\",\n    \"NCBI:NC_000013.11\",\n
+        \   \"refseq:NC_000013.11\",\n    \"SEGUID:2oDBty0yKV9wHo7gg+Bt+fPgi5o\",\n
+        \   \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n    \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n
+        \   \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n    \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n
+        \ ],\n  \"alphabet\": \"ACGKNTY\",\n  \"length\": 114364328\n}\n"
+    headers:
+      Connection:
+      - close
+      Content-Length:
+      - '1002'
+      Content-Type:
+      - application/json
+      Date:
+      - Thu, 17 Aug 2023 03:03:25 GMT
+      Server:
+      - Werkzeug/2.2.3 Python/3.11.4
+    status:
+      code: 200
+      message: OK
+- request:
+    body: null
+    headers:
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      User-Agent:
+      - python-requests/2.31.0
     method: GET
     uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT
   response:
@@ -35,9 +77,9 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Mon, 19 Sep 2022 15:07:31 GMT
+      - Thu, 17 Aug 2023 03:03:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.11.4
     status:
       code: 200
       message: OK
@@ -51,7 +93,7 @@ interactions:
       Connection:
       - keep-alive
       User-Agent:
-      - python-requests/2.28.1
+      - python-requests/2.31.0
     method: GET
     uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32936731&end=32936732
   response:
@@ -65,9 +107,9 @@ interactions:
       Content-Type:
       - text/plain; charset=utf-8
       Date:
-      - Mon, 19 Sep 2022 15:07:31 GMT
+      - Thu, 17 Aug 2023 03:03:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.11.4
     status:
       code: 200
       message: OK
@@ -81,7 +123,7 @@ interactions:
       Connection:
       - keep-alive
       User-Agent:
-      - python-requests/2.28.1
+      - python-requests/2.31.0
     method: GET
     uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT
   response:
@@ -107,9 +149,9 @@ interactions:
       Content-Type:
       - application/json
       Date:
-      - Mon, 19 Sep 2022 15:07:32 GMT
+      - Thu, 17 Aug 2023 03:03:25 GMT
       Server:
-      - Werkzeug/2.2.2 Python/3.10.4
+      - Werkzeug/2.2.3 Python/3.11.4
     status:
       code: 200
       message: OK