varcode 9.2.1__tar.gz → 9.2.2__tar.gz

{varcode-9.2.1/varcode.egg-info → varcode-9.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 9.2.1
+Version: 9.2.2
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode

varcode-9.2.2/tests/test_sv_tabular_metadata.py

@@ -0,0 +1,69 @@
+"""Structural records must never masquerade as placeholder SNVs (#417)."""
+
+import pickle
+
+import pytest
+
+from varcode import StructuralVariant, Variant, VariantCollection
+from varcode.csv_helpers import STRUCTURAL_VARIANT_COLUMNS
+from varcode.effects import EffectCollection, Intergenic
+
+
+@pytest.mark.parametrize("ref", ["A", "C", "G", "T", "N"])
+@pytest.mark.parametrize("kind,alt", [
+    ("DEL", "<DEL>"), ("DUP", "<DUP>"), ("INV", "<INV>"),
+    ("CNV", "<CN3>"), ("INS", "<INS:ME:ALU>"),
+    ("BND", "G[2:200["), ("BND", ".ACGT"), ("INS", "ACGT"),
+])
+def test_actual_alleles_and_no_small_edit_flags(ref, kind, alt):
+    sv = StructuralVariant("1", 100, kind, end=200, ref=ref, alt=alt)
+    assert sv.start == sv.original_start == 100
+    assert sv.ref == sv.original_ref == ref
+    assert sv.alt == sv.original_alt == sv.symbolic_alt == alt
+    for name in ["is_snv", "is_indel", "is_insertion", "is_deletion",
+                 "is_transition", "is_transversion"]:
+        assert getattr(sv, name) is False
+    assert sv.is_structural
+    for restored in [StructuralVariant.from_json(sv.to_json()), pickle.loads(pickle.dumps(sv))]:
+        assert restored == sv
+        assert (restored.ref, restored.alt) == (ref, alt)
+
+
+def examples():
+    snv = Variant("1", 50, "C", "T")
+    sv = StructuralVariant("1", 100, "DEL", end=200, ref="T", affected_start=101,
+                           mate_contig="2", mate_start=300)
+    for variant in [snv, sv]:
+        variant._gene_names = []
+        variant._gene_ids = []
+    return snv, sv
+
+
+@pytest.mark.parametrize("effects", [False, True])
+def test_mixed_tables_retain_structural_coordinates(effects, tmp_path):
+    snv, sv = examples()
+    collection = (EffectCollection([Intergenic(snv), Intergenic(sv)], sort_key=False)
+                  if effects else VariantCollection([snv, sv]))
+    df = collection.to_dataframe()
+    assert list(df.columns) == list(collection._DATAFRAME_COLUMNS + STRUCTURAL_VARIANT_COLUMNS)
+    row = df.iloc[1]
+    assert (row["ref"], row["alt"], row["sv_type"]) == ("T", "<DEL>", "DEL")
+    assert (row["start"], row["end"], row["affected_start"], row["affected_end"]) == (100, 200, 101, 200)
+    assert (row["mate_contig"], row["mate_start"]) == ("2", 300)
+    if effects:
+        assert not row["is_snv"] and not row["is_transition"] and not row["is_transversion"]
+        assert df.iloc[0]["is_snv"] and df.iloc[0]["is_transition"]
+    path = tmp_path / "mixed.csv"
+    collection.to_csv(str(path))
+    with pytest.raises(ValueError, match="Structural rows cannot be reconstructed"):
+        type(collection).from_csv(str(path))
+
+
+@pytest.mark.parametrize("effects", [False, True])
+@pytest.mark.parametrize("empty", [False, True])
+def test_point_only_and_empty_schemas_unchanged(effects, empty):
+    snv, _ = examples()
+    variants = [] if empty else [snv]
+    collection = (EffectCollection([Intergenic(v) for v in variants]) if effects
+                  else VariantCollection(variants))
+    assert tuple(collection.to_dataframe().columns) == collection._DATAFRAME_COLUMNS

{varcode-9.2.1 → varcode-9.2.2}/varcode/csv_helpers.py

@@ -39,6 +39,18 @@ HEADER_PREFIX = "#"
 # openvax/varcode#274.
 CONTIG_COLUMN_ALIASES = ("contig", "chr")
 
+STRUCTURAL_VARIANT_COLUMNS = (
+    "sv_type", "end", "mate_contig", "mate_start", "affected_start", "affected_end",
+)
+
+
+def reject_structural_csv(df):
+    """CSV summaries do not encode enough state to restore structural effects."""
+    if "sv_type" in df and df["sv_type"].fillna("").ne("").any():
+        raise ValueError(
+            "Structural rows cannot be reconstructed from CSV summaries. "
+            "Retain the original VCF/JSON variants and RNA evidence instead.")
+
 
 def resolve_contig_column(columns):
     """Return the first of :data:`CONTIG_COLUMN_ALIASES` that appears in

{varcode-9.2.1 → varcode-9.2.2}/varcode/effects/effect_collection.py

@@ -17,7 +17,9 @@ from sercol import Collection
 
 from ..csv_helpers import (
     CONTIG_COLUMN_ALIASES,
+    STRUCTURAL_VARIANT_COLUMNS,
     read_metadata_header,
+    reject_structural_csv,
     resolve_contig_column,
     warn_on_version_drift,
     write_metadata_header,
@@ -344,6 +346,8 @@ class EffectCollection(Collection):
 
     def to_dataframe(self):
         """Build a dataframe from the effect collection."""
+        structural_columns = STRUCTURAL_VARIANT_COLUMNS if any(
+            getattr(e.variant, "is_structural", False) for e in self) else ()
         # list of properties to extract from Variant objects if they're
         # not None
         variant_properties = [
@@ -354,7 +358,7 @@ class EffectCollection(Collection):
             "is_snv",
             "is_transversion",
             "is_transition"
-        ]
+        ] + list(structural_columns)
 
         def row_from_effect(effect):
             row = OrderedDict()
@@ -375,7 +379,7 @@ class EffectCollection(Collection):
         # CSV round-trip doesn't have to special-case len == 0.
         return pd.DataFrame.from_records(
             [row_from_effect(effect) for effect in self],
-            columns=self._DATAFRAME_COLUMNS,
+            columns=self._DATAFRAME_COLUMNS + structural_columns,
         )
 
     def to_csv(self, path, include_header=True):
@@ -485,6 +489,7 @@ class EffectCollection(Collection):
         # dtype is a no-op for whichever column is absent.
         df = pd.read_csv(
             path, comment="#", dtype={"chr": str, "contig": str})
+        reject_structural_csv(df)
         contig_col = resolve_contig_column(df.columns)
         if contig_col is None:
             raise ValueError(

{varcode-9.2.1 → varcode-9.2.2}/varcode/structural_variant.py

@@ -242,6 +242,15 @@ class StructuralVariant(Variant):
         event coordinates include a retained padding base.
     """
 
+    # These flags describe literal small edits, not event classes. Consumers
+    # must use is_structural/sv_type instead of interpreting symbolic alleles.
+    is_snv = False
+    is_indel = False
+    is_insertion = False
+    is_deletion = False
+    is_transition = False
+    is_transversion = False
+
     __slots__ = (
         "sv_type",
         "mate_contig",
@@ -288,14 +297,14 @@ class StructuralVariant(Variant):
 
         # Initialize the base Variant with a placeholder ref/alt so the
         # nucleotide-normalization path doesn't reject <DEL>-style
-        # symbolic alleles. The original symbolic ALT is preserved in
-        # ``_sv_alt``; :attr:`alt` returns it via a property override.
+        # symbolic alleles. Restore the actual record fields below; placeholder
+        # normalization must not leak into public alleles or exports (#417).
         Variant.__init__(
             self,
             contig=contig,
             start=start,
             ref=ref if ref else "N",
-            alt="A" if ref == "N" else "A",  # placeholder, overridden below
+            alt="A",
             genome=genome,
             ensembl=ensembl,
             allow_extended_nucleotides=True,
@@ -325,6 +334,9 @@ class StructuralVariant(Variant):
         # Preserve the original symbolic ALT string so round-tripping
         # and downstream consumers see what the VCF said.
         self._sv_alt = alt if alt is not None else "<%s>" % sv_type
+        self.ref = self.original_ref
+        self.alt = self.original_alt = self._sv_alt
+        self.start = self.original_start = int(start)
 
         # Caches, like Variant's overlapping-gene / transcript caches:
         # the junction list derived from the fields above, and results

{varcode-9.2.1 → varcode-9.2.2}/varcode/variant_collection.py

@@ -19,7 +19,9 @@ from .effects import EffectCollection
 from .common import memoize
 from .csv_helpers import (
     CONTIG_COLUMN_ALIASES,
+    STRUCTURAL_VARIANT_COLUMNS,
     read_metadata_header,
+    reject_structural_csv,
     resolve_contig_column,
     warn_on_version_drift,
     write_metadata_header,
@@ -434,8 +436,10 @@ class VariantCollection(Collection):
 
     def to_dataframe(self):
         """Build a DataFrame from this variant collection."""
+        structural_columns = STRUCTURAL_VARIANT_COLUMNS if any(
+            getattr(v, "is_structural", False) for v in self) else ()
         def row_from_variant(variant):
-            return OrderedDict([
+            row = OrderedDict([
                 ("chr", variant.contig),
                 ("start", variant.original_start),
                 ("ref", variant.original_ref),
@@ -443,11 +447,13 @@ class VariantCollection(Collection):
                 ("gene_name", ";".join(variant.gene_names)),
                 ("gene_id", ";".join(variant.gene_ids))
             ])
+            row.update((name, getattr(variant, name, None)) for name in structural_columns)
+            return row
         rows = [row_from_variant(v) for v in self]
         # Always return a DataFrame with the expected columns, even
         # when empty, so downstream code (CSV round-trip, joins) doesn't
         # have to special-case len == 0.
-        return pd.DataFrame.from_records(rows, columns=self._DATAFRAME_COLUMNS)
+        return pd.DataFrame.from_records(rows, columns=self._DATAFRAME_COLUMNS + structural_columns)
 
     def to_csv(self, path, include_header=True):
         """Write this collection to CSV.
@@ -541,6 +547,7 @@ class VariantCollection(Collection):
         # dtype is a no-op for whichever column is absent.
         df = pd.read_csv(
             path, comment="#", dtype={"chr": str, "contig": str})
+        reject_structural_csv(df)
         contig_col = resolve_contig_column(df.columns)
         if contig_col is None:
             raise ValueError(

varcode-9.2.2/varcode/version.py

@@ -0,0 +1 @@
+__version__ = "9.2.2"

{varcode-9.2.1 → varcode-9.2.2/varcode.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 9.2.1
+Version: 9.2.2
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode

{varcode-9.2.1 → varcode-9.2.2}/varcode.egg-info/SOURCES.txt

@@ -68,6 +68,7 @@ tests/test_stop_codon_classification_bugs.py
 tests/test_string_helpers.py
 tests/test_structural_variant_annotator.py
 tests/test_structural_variants.py
+tests/test_sv_tabular_metadata.py
 tests/test_symbolic_alleles.py
 tests/test_symbolic_sv_padding.py
 tests/test_timings.py

varcode-9.2.1/varcode/version.py

@@ -1 +0,0 @@
-__version__ = "9.2.1"