varcode 9.2.3__tar.gz → 9.2.5__tar.gz

varcode-9.2.5/PKG-INFO

@@ -0,0 +1,106 @@
+Metadata-Version: 2.4
+Name: varcode
+Version: 9.2.5
+Summary: Variant annotation in Python
+Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
+Project-URL: Homepage, https://github.com/openvax/varcode
+Project-URL: Bug Tracker, https://github.com/openvax/varcode/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<3.0.0,>=2.0.0
+Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: pyensembl>=2.6.4
+Requires-Dist: memoized_property>=1.0.2
+Requires-Dist: serializable>=1.1.0
+Requires-Dist: sercol>=0.1.4
+Provides-Extra: rna
+Requires-Dist: pysam>=0.21; extra == "rna"
+Dynamic: license-file
+
+[![Tests](https://github.com/openvax/varcode/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/varcode/actions/workflows/tests.yml)
+[![Coverage Status](https://coveralls.io/repos/openvax/varcode/badge.svg?branch=main&service=github)](https://coveralls.io/github/openvax/varcode?branch=main)
+[![PyPI](https://img.shields.io/pypi/v/varcode.svg?maxAge=1000)](https://pypi.python.org/pypi/varcode/)
+[![PyPI downloads](https://img.shields.io/pypi/dm/varcode.svg)](https://pypistats.org/packages/varcode)
+
+# Varcode
+
+Varcode helps you work with genomic variants in Python and predict their effects
+on genes, transcripts, and protein sequences.
+
+Load variants from VCF or MAF files, annotate them, and inspect the results.
+The same interface handles small variants and structural variants; optional
+germline, phasing, and RNA evidence can refine predictions.
+
+## Installation
+
+Requires Python 3.9 or later:
+
+```bash
+pip install varcode
+pyensembl install --release 81 --species human
+```
+
+The second command downloads the annotation and transcript sequences for the
+GRCh38 example below. Release 81 is pinned for reproducibility, not a requirement
+to use that release for your own data. Choose an annotation matching your
+input's genome build; see [reference setup](https://openvax.github.io/varcode/getting_started/#reference-data).
+
+<a id="example"></a>
+
+## Quick start
+
+Predict the effect of a single GRCh38 variant on a CFTR transcript:
+
+```python
+from varcode import Variant
+
+variant = Variant("7", 117_531_100, "T", "A", genome=81)
+transcript = variant.genome.transcript_by_id("ENST00000003084")
+effect = variant.effect_on_transcript(transcript)
+
+print(effect.short_description)  # p.L159M
+protein = effect.mutant_protein_sequence
+```
+
+For a VCF called against the same genome build:
+
+```python
+from varcode import load_vcf
+
+variants = load_vcf("variants.vcf", genome=81)
+effects = variants.effects()
+for variant, effect in effects.top_priority_effect_per_variant().items():
+    print(variant.short_description, effect.short_description)
+```
+
+A variant can affect several transcripts. Priority is a summary of predicted
+consequence, not proof of expression or pathogenicity. A protein sequence may be
+unavailable for unresolved effects.
+
+<a id="further-reading"></a>
+
+## Learn more
+
+Start with the [getting-started guide](https://openvax.github.io/varcode/getting_started/)
+for file loading, result access, and saving a table. Then follow the
+[task guides](https://openvax.github.io/varcode/#find-your-next-task) for sample
+filtering, structural variants, phasing, and RNA evidence.
+
+<a id="effect-types"></a>
+<a id="coordinate-system"></a>
+
+Detailed [effect types](https://openvax.github.io/varcode/effect_types/),
+[coordinate conventions](https://openvax.github.io/varcode/getting_started/#coordinate-conventions),
+and the [API reference](https://openvax.github.io/varcode/api/) live in the docs.
+
+For bugs or questions, [open an issue](https://github.com/openvax/varcode/issues).
+Contributions are welcome; see [CONTRIBUTING.md](CONTRIBUTING.md) and the
+[changelog](CHANGELOG.md).

varcode-9.2.5/README.md

@@ -0,0 +1,79 @@
+[![Tests](https://github.com/openvax/varcode/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/varcode/actions/workflows/tests.yml)
+[![Coverage Status](https://coveralls.io/repos/openvax/varcode/badge.svg?branch=main&service=github)](https://coveralls.io/github/openvax/varcode?branch=main)
+[![PyPI](https://img.shields.io/pypi/v/varcode.svg?maxAge=1000)](https://pypi.python.org/pypi/varcode/)
+[![PyPI downloads](https://img.shields.io/pypi/dm/varcode.svg)](https://pypistats.org/packages/varcode)
+
+# Varcode
+
+Varcode helps you work with genomic variants in Python and predict their effects
+on genes, transcripts, and protein sequences.
+
+Load variants from VCF or MAF files, annotate them, and inspect the results.
+The same interface handles small variants and structural variants; optional
+germline, phasing, and RNA evidence can refine predictions.
+
+## Installation
+
+Requires Python 3.9 or later:
+
+```bash
+pip install varcode
+pyensembl install --release 81 --species human
+```
+
+The second command downloads the annotation and transcript sequences for the
+GRCh38 example below. Release 81 is pinned for reproducibility, not a requirement
+to use that release for your own data. Choose an annotation matching your
+input's genome build; see [reference setup](https://openvax.github.io/varcode/getting_started/#reference-data).
+
+<a id="example"></a>
+
+## Quick start
+
+Predict the effect of a single GRCh38 variant on a CFTR transcript:
+
+```python
+from varcode import Variant
+
+variant = Variant("7", 117_531_100, "T", "A", genome=81)
+transcript = variant.genome.transcript_by_id("ENST00000003084")
+effect = variant.effect_on_transcript(transcript)
+
+print(effect.short_description)  # p.L159M
+protein = effect.mutant_protein_sequence
+```
+
+For a VCF called against the same genome build:
+
+```python
+from varcode import load_vcf
+
+variants = load_vcf("variants.vcf", genome=81)
+effects = variants.effects()
+for variant, effect in effects.top_priority_effect_per_variant().items():
+    print(variant.short_description, effect.short_description)
+```
+
+A variant can affect several transcripts. Priority is a summary of predicted
+consequence, not proof of expression or pathogenicity. A protein sequence may be
+unavailable for unresolved effects.
+
+<a id="further-reading"></a>
+
+## Learn more
+
+Start with the [getting-started guide](https://openvax.github.io/varcode/getting_started/)
+for file loading, result access, and saving a table. Then follow the
+[task guides](https://openvax.github.io/varcode/#find-your-next-task) for sample
+filtering, structural variants, phasing, and RNA evidence.
+
+<a id="effect-types"></a>
+<a id="coordinate-system"></a>
+
+Detailed [effect types](https://openvax.github.io/varcode/effect_types/),
+[coordinate conventions](https://openvax.github.io/varcode/getting_started/#coordinate-conventions),
+and the [API reference](https://openvax.github.io/varcode/api/) live in the docs.
+
+For bugs or questions, [open an issue](https://github.com/openvax/varcode/issues).
+Contributions are welcome; see [CONTRIBUTING.md](CONTRIBUTING.md) and the
+[changelog](CHANGELOG.md).

varcode-9.2.5/tests/test_bnd_retained_segments.py

@@ -0,0 +1,111 @@
+"""A BND fallback describes only its retained reference fragment (#447)."""
+
+import pytest
+from pyensembl import cached_release
+
+from varcode import StructuralVariant, parse_symbolic_alt
+from varcode.effects import TranslocationToIntergenic
+from varcode.effects.structural import _build_translocation_mutant_transcript
+
+
+@pytest.fixture(params=["ENST00000003084", "ENST00000357654"])
+def transcript(request):
+    return cached_release(81).transcript_by_id(request.param)
+
+
+def expected_offsets(transcript, position, side):
+    """Independent per-base oracle in transcript order, including the anchor."""
+    positions = [p for exon in transcript.exons
+                 for p in (range(exon.start, exon.end + 1) if transcript.strand == "+"
+                           else range(exon.end, exon.start - 1, -1))]
+    kept = [i for i, p in enumerate(positions)
+            if (p <= position if side == "left" else p >= position)]
+    return min(kept), max(kept) + 1
+
+
+@pytest.mark.parametrize("alt,side", [
+    ("N[22:15500000[", "left"), ("N]22:15500000]", "left"),
+    ("[22:15500000[N", "right"), ("]22:15500000]N", "right"),
+    ("ACGT.", "left"), (".ACGT", "right"),
+])
+@pytest.mark.parametrize("location", ["exonic", "exon_start", "exon_end", "intronic"])
+def test_both_strands_and_local_sides(transcript, alt, side, location):
+    # An interior exon also permits meaningful suffix/prefix comparisons.
+    exon = transcript.exons[2]
+    if location == "exonic":
+        position = (exon.start + exon.end) // 2
+    elif location == "exon_start":
+        position = exon.start
+    elif location == "exon_end":
+        position = exon.end
+    else:
+        other = transcript.exons[3]
+        position = ((exon.end + other.start) // 2 if transcript.strand == "+"
+                    else (other.end + exon.start) // 2)
+    sv = parse_symbolic_alt(transcript.contig, position, "N", alt,
+                            genome=transcript.genome)
+    effect = sv.effect_on_transcript(transcript)
+    assert isinstance(effect, TranslocationToIntergenic)
+    mt = effect.mutant_transcript
+    assert mt is not None
+    (segment,) = mt.reference_segments
+    assert segment.source is transcript
+    assert (segment.start, segment.end) == expected_offsets(transcript, position, side)
+    assert segment.strand == "+"  # source is already oriented transcript cDNA
+    five_prime = (side == "left") == (transcript.strand == "+")
+    assert segment.label == ("translocation_5p" if five_prime else "translocation_3p")
+    assert segment.length < len(transcript.sequence)
+    assert mt.cdna_sequence is None
+    assert mt.mutant_protein_sequence is None
+    assert mt.evidence["sequence_status"] == "retained_reference_fragment"
+
+
+def test_cftr_regression_keeps_51_bases_not_entire_transcript():
+    tx = cached_release(81).transcript_by_id("ENST00000003084")
+    sv = parse_symbolic_alt("7", tx.exons[0].start + 50, "N", "N]22:15500000]",
+                            genome=tx.genome)
+    mt = sv.effect_on_transcript(tx).mutant_transcript
+    (segment,) = mt.reference_segments
+    assert (segment.start, segment.end) == (0, 51)
+    assert segment.source.sequence[segment.start:segment.end] == tx.sequence[:51]
+
+
+@pytest.mark.parametrize("alt", [None, "<BND>", "N[?:?[", "N[22:15500000]", ".", "N.N"])
+def test_unknown_local_orientation_is_unresolved(transcript, alt):
+    sv = StructuralVariant(transcript.contig, transcript.exons[0].start + 5,
+                           "BND", alt=alt, genome=transcript.genome)
+    assert sv.effect_on_transcript(transcript).mutant_transcript is None
+
+
+@pytest.mark.parametrize("orientation", ["[[", "]]"])
+def test_mate_orientation_does_not_determine_local_side(transcript, orientation):
+    sv = StructuralVariant(transcript.contig, transcript.exons[0].start + 5,
+                           "BND", mate_contig="22", mate_start=15_500_000,
+                           mate_orientation=orientation, genome=transcript.genome)
+    with pytest.warns(UserWarning, match="can't read the breakend orientation"):
+        effect = sv.effect_on_transcript(transcript)
+    assert isinstance(effect, TranslocationToIntergenic)
+    assert effect.mutant_transcript is None
+
+
+@pytest.mark.parametrize("location", ["before", "after", "wrong_contig"])
+def test_unrelated_transcript_does_not_supply_a_segment(transcript, location):
+    position = {"before": transcript.start - 1, "after": transcript.end + 1,
+                "wrong_contig": transcript.start + 5}[location]
+    contig = "1" if location == "wrong_contig" else transcript.contig
+    sv = StructuralVariant(contig, position, "BND", alt="N.", genome=transcript.genome)
+    assert _build_translocation_mutant_transcript(sv, transcript) is None
+
+
+@pytest.mark.parametrize("alt", ["N]22:15500000]", "]22:15500000]N", "N.", ".N", "<BND>"])
+def test_supplied_assembly_is_unchanged(transcript, alt):
+    assembly = "ATGGCTTAA"
+    sv = StructuralVariant(transcript.contig, transcript.exons[0].start + 5,
+                           "BND", alt=alt, alt_assembly=assembly, genome=transcript.genome)
+    mt = sv.effect_on_transcript(transcript).mutant_transcript
+    assert mt.cdna_sequence == assembly
+    assert mt.mutant_protein_sequence is None
+    assert mt.evidence == {"source": "alt_assembly"}
+    (segment,) = mt.reference_segments
+    assert segment.source.sequence == assembly
+    assert (segment.start, segment.end, segment.label) == (0, len(assembly), "alt_assembly")

varcode-9.2.5/tests/test_documentation_examples.py

@@ -0,0 +1,127 @@
+"""Keep the reader-facing examples executable, using their actual Markdown."""
+
+from pathlib import Path
+import re
+import shutil
+
+import pytest
+from pyensembl import cached_release
+
+import varcode
+from varcode import EffectCandidate, StructuralVariant, Variant
+from varcode.effect_hypotheses import RealizedEffectCandidate
+
+
+ROOT = Path(__file__).resolve().parents[1]
+
+
+def _blocks(path, heading=None):
+    text = (ROOT / path).read_text()
+    if heading is not None:
+        text = text.split(heading + "\n", 1)[1]
+    return re.findall(r"```python\n(.*?)```", text, re.S)
+
+
+def _run(blocks, namespace=None):
+    namespace = {} if namespace is None else namespace
+    for block in blocks:
+        exec(compile(block, "documentation example", "exec"), namespace)
+    return namespace
+
+
+@pytest.fixture
+def input_directory(tmp_path, monkeypatch):
+    for fixture in (ROOT / "tests/data/documentation").glob("*.vcf"):
+        shutil.copy(fixture, tmp_path / fixture.name)
+    shutil.copy(tmp_path / "variants.vcf", tmp_path / "tumor.vcf")
+    monkeypatch.chdir(tmp_path)
+    return tmp_path
+
+
+@pytest.mark.parametrize("path,count", [
+    ("README.md", 2),
+    ("docs/getting_started.md", 4),
+    ("docs/index.md", 1),
+    ("docs/effect_annotation.md", 3),
+    ("docs/structural_variants.md", 1),
+    ("docs/transforms.md", 1),
+    ("docs/germline.md", 1),
+])
+def test_documentation_first_steps(path, count, input_directory):
+    namespace = _run(_blocks(path)[:count])
+    if path == "docs/transforms.md":
+        assert len(namespace["paired"]) == len(namespace["normalized"]) == 1
+    else:
+        assert len(namespace["effects"]) > 0
+    if path in ("README.md", "docs/getting_started.md"):
+        assert namespace["protein"][158] == "M"
+    if path == "docs/getting_started.md":
+        assert (input_directory / "effects.csv").is_file()
+    if path == "docs/structural_variants.md":
+        assert namespace["variants"][0].is_structural
+
+
+def test_documentation_germline_scenarios():
+    namespace = _run(_blocks(
+        "docs/germline.md", "## Concrete example: same codon, three scenarios")[:4])
+    assert namespace["eff_cis"].short_description == "p.S159T"
+    assert namespace["eff_trans"].short_description == "p.L159M"
+    assert {c.effect.short_description for c in namespace["eff"].candidates} == {
+        "p.S159T", "p.L159M"}
+
+    _run(_blocks("docs/germline.md", "## Loss of heterozygosity (LOH)")[:1],
+         namespace)
+    assert any(getattr(effect, "is_loh", False)
+               for effect in namespace["overlap"].effects(germline=namespace["ctx"]))
+
+    validation = _blocks("docs/germline.md", "## Cross-VCF build mismatch")[:1]
+    _run(validation, namespace)
+    namespace["ctx"] = varcode.GermlineContext.from_variants(
+        [namespace["germline"]], reference_name="GRCh37")
+    with pytest.raises(varcode.GenomeBuildMismatchError):
+        _run(validation, namespace)
+
+
+def test_documentation_splice_accessors():
+    text = (ROOT / "docs/effect_annotation.md").read_text()
+    section = text.split("### The `SpliceOutcomeSet` shape\n", 1)[1]
+    section = section.split("### RNA evidence reconciliation\n", 1)[0]
+    blocks = re.findall(r"```python\n(.*?)```", section, re.S)
+    namespace = _run(blocks[:1])
+    namespace["effect"] = namespace["splice_set"]
+    _run(blocks[1:], namespace)
+    assert isinstance(namespace["splice_set"], varcode.SpliceOutcomeSet)
+    assert namespace["coding"] is not None
+
+
+@pytest.mark.parametrize("kind", ["point", "BND", "CNV"])
+def test_documentation_experimental_result_access(kind):
+    genome = cached_release(81)
+    transcript = genome.transcript_by_id("ENST00000003084")
+    if kind == "point":
+        variant = Variant("7", 117531100, "T", "A", genome)
+    elif kind == "BND":
+        variant = StructuralVariant(
+            "7", transcript.start + 50, "BND", alt="N]22:15500000]",
+            mate_contig="22", mate_start=15500000, genome=genome)
+    else:
+        variant = StructuralVariant(
+            "7", transcript.start + 50, "CNV", end=transcript.start + 100,
+            genome=genome)
+    namespace = dict(varcode=varcode, variant=variant, transcript=transcript)
+    advanced_blocks = _blocks("docs/effect_annotation.md",
+                              "## Advanced: annotators and implementation limits")
+    assert "comparison =" in advanced_blocks[0]
+    assert "candidate.outcomes" in advanced_blocks[1]
+    _run(advanced_blocks[:2], namespace)
+    _run(_blocks("docs/effect_annotation.md", "## Read an effect")[:1], namespace)
+    candidates = getattr(namespace["experimental"], "candidates", ())
+    if kind == "point":
+        assert candidates and all(isinstance(c, RealizedEffectCandidate)
+                                  for c in candidates)
+        assert namespace["protein"][158] == "M"
+    elif kind == "BND":
+        assert candidates and all(isinstance(c, EffectCandidate) for c in candidates)
+    else:
+        assert not candidates
+        assert isinstance(namespace["experimental"], varcode.Unresolved)

{varcode-9.2.3 → varcode-9.2.5}/varcode/effects/structural.py

@@ -35,7 +35,7 @@ from .effect_helpers import exon_length
 from ..mutant_transcript import MutantTranscript, ReferenceSegment
 # Existing assembled-SV pickles use this private module path.
 from ..mutant_transcript import _AssembledAllele  # noqa: F401
-from ..sv_allele_parser import breakend_sides
+from ..sv_allele_parser import breakend_sides, _breakend_local_side
 
 
 # --------------------------------------------------------------------
@@ -501,23 +501,29 @@ def _build_fusion_mutant_transcript(
 
 
 def _build_translocation_mutant_transcript(variant, transcript):
-    """Build a :class:`MutantTranscript` for a BND classified as
-    :class:`TranslocationToIntergenic`.
+    """Describe only the retained local reference fragment of a BND.
 
-    One segment covering the (this-side) transcript up to the
-    breakpoint. Intergenic space beyond the breakpoint isn't
-    representable as a transcript source; #338 and #341 extend this
-    with caller-supplied genomic intervals / long-read assemblies.
+    The other side and full mutant cDNA/protein remain unknown. Without
+    local orientation or a breakpoint on this transcript, no fragment can
+    be established. Supplied assemblies are handled by the caller.
     """
+    side = _breakend_local_side(variant.symbolic_alt)
+    if (side is None or str(variant.contig) != str(transcript.contig)
+            or not transcript.start <= variant.start <= transcript.end):
+        return None
+    keep_five_prime = _retains_five_prime_end(transcript, side)
+    cut = _cdna_cut(transcript, variant.start, keep_five_prime)
     full_len = len(str(transcript.sequence))
+    start, end = (0, cut) if keep_five_prime else (cut, full_len)
     segments = (
         ReferenceSegment(
-            source=transcript, start=0, end=full_len,
-            strand="+", label="translocation_5p"),)
+            source=transcript, start=start, end=end, strand="+",
+            label="translocation_5p" if keep_five_prime else "translocation_3p"),)
     return MutantTranscript(
         reference_transcript=transcript,
         reference_segments=segments,
         cdna_sequence=None,
+        evidence={"sequence_status": "retained_reference_fragment"},
         annotator_name="structural_variant")
 
 

{varcode-9.2.3 → varcode-9.2.5}/varcode/mutant_transcript.py

@@ -232,7 +232,10 @@ class MutantTranscript(DataclassSerializable):
     strand segments), produce the mutant cDNA. ``None`` for the
     point-variant shape; a fusion's segments would be
     ``(5p_partner_segment, 3p_partner_segment)``. Coordinates are
-    in each segment's own reference system."""
+    in each segment's own reference system. A partial structural model may
+    describe only a retained reference fragment: its producer identifies this
+    in ``evidence`` and leaves the full ``cdna_sequence`` unknown. Concatenating
+    those partial segments does not establish a full allele."""
 
     cdna_sequence: Optional[str] = None
     """The mutated spliced mRNA, when computed. ``None`` if the

{varcode-9.2.3 → varcode-9.2.5}/varcode/sv_allele_parser.py

@@ -78,6 +78,17 @@ def breakend_sides(alt):
     return this_side, mate_side
 
 
+def _breakend_local_side(alt):
+    """The retained local side, including single breakends with no mate."""
+    sides = breakend_sides(alt)
+    if sides is not None:
+        return sides[0]
+    single = _SINGLE_BREAKEND_RE.match(alt or "")
+    if single is not None:
+        return "right" if single.group("joined_before") else "left"
+    return None
+
+
 def _extract_info(info, key):
     """Pull an INFO field value, handling list-of-ints from CIPOS /
     CIEND and plain ints/strings otherwise. Returns ``None`` if

{varcode-9.2.3 → varcode-9.2.5}/varcode/variant.py

@@ -464,7 +464,7 @@ class Variant(Serializable):
             :func:`varcode.use_annotator`). String names are resolved
             against the registry. See openvax/varcode#271.
 
-        phase_resolver : PhaseResolver or None
+        phase_resolver : resolver object or None
             Optional phase-evidence source (typically a
             :class:`~varcode.phasing.MolecularPhaseResolver` wrapping an
             upstream RNA-phasing tool, or

{varcode-9.2.3 → varcode-9.2.5}/varcode/variant_collection.py

@@ -140,7 +140,7 @@ class VariantCollection(Collection):
             the collection. See :meth:`Variant.effects` and
             openvax/varcode#271.
 
-        phase_resolver : PhaseResolver or None
+        phase_resolver : resolver object or None
             Optional phase-evidence source (e.g. a
             :class:`~varcode.phasing.MolecularPhaseResolver` wrapping an
             upstream RNA-phasing tool, or

varcode-9.2.5/varcode/version.py

@@ -0,0 +1 @@
+__version__ = "9.2.5"

varcode-9.2.5/varcode.egg-info/PKG-INFO

@@ -0,0 +1,106 @@
+Metadata-Version: 2.4
+Name: varcode
+Version: 9.2.5
+Summary: Variant annotation in Python
+Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
+Project-URL: Homepage, https://github.com/openvax/varcode
+Project-URL: Bug Tracker, https://github.com/openvax/varcode/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<3.0.0,>=2.0.0
+Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: pyensembl>=2.6.4
+Requires-Dist: memoized_property>=1.0.2
+Requires-Dist: serializable>=1.1.0
+Requires-Dist: sercol>=0.1.4
+Provides-Extra: rna
+Requires-Dist: pysam>=0.21; extra == "rna"
+Dynamic: license-file
+
+[![Tests](https://github.com/openvax/varcode/actions/workflows/tests.yml/badge.svg)](https://github.com/openvax/varcode/actions/workflows/tests.yml)
+[![Coverage Status](https://coveralls.io/repos/openvax/varcode/badge.svg?branch=main&service=github)](https://coveralls.io/github/openvax/varcode?branch=main)
+[![PyPI](https://img.shields.io/pypi/v/varcode.svg?maxAge=1000)](https://pypi.python.org/pypi/varcode/)
+[![PyPI downloads](https://img.shields.io/pypi/dm/varcode.svg)](https://pypistats.org/packages/varcode)
+
+# Varcode
+
+Varcode helps you work with genomic variants in Python and predict their effects
+on genes, transcripts, and protein sequences.
+
+Load variants from VCF or MAF files, annotate them, and inspect the results.
+The same interface handles small variants and structural variants; optional
+germline, phasing, and RNA evidence can refine predictions.
+
+## Installation
+
+Requires Python 3.9 or later:
+
+```bash
+pip install varcode
+pyensembl install --release 81 --species human
+```
+
+The second command downloads the annotation and transcript sequences for the
+GRCh38 example below. Release 81 is pinned for reproducibility, not a requirement
+to use that release for your own data. Choose an annotation matching your
+input's genome build; see [reference setup](https://openvax.github.io/varcode/getting_started/#reference-data).
+
+<a id="example"></a>
+
+## Quick start
+
+Predict the effect of a single GRCh38 variant on a CFTR transcript:
+
+```python
+from varcode import Variant
+
+variant = Variant("7", 117_531_100, "T", "A", genome=81)
+transcript = variant.genome.transcript_by_id("ENST00000003084")
+effect = variant.effect_on_transcript(transcript)
+
+print(effect.short_description)  # p.L159M
+protein = effect.mutant_protein_sequence
+```
+
+For a VCF called against the same genome build:
+
+```python
+from varcode import load_vcf
+
+variants = load_vcf("variants.vcf", genome=81)
+effects = variants.effects()
+for variant, effect in effects.top_priority_effect_per_variant().items():
+    print(variant.short_description, effect.short_description)
+```
+
+A variant can affect several transcripts. Priority is a summary of predicted
+consequence, not proof of expression or pathogenicity. A protein sequence may be
+unavailable for unresolved effects.
+
+<a id="further-reading"></a>
+
+## Learn more
+
+Start with the [getting-started guide](https://openvax.github.io/varcode/getting_started/)
+for file loading, result access, and saving a table. Then follow the
+[task guides](https://openvax.github.io/varcode/#find-your-next-task) for sample
+filtering, structural variants, phasing, and RNA evidence.
+
+<a id="effect-types"></a>
+<a id="coordinate-system"></a>
+
+Detailed [effect types](https://openvax.github.io/varcode/effect_types/),
+[coordinate conventions](https://openvax.github.io/varcode/getting_started/#coordinate-conventions),
+and the [API reference](https://openvax.github.io/varcode/api/) live in the docs.
+
+For bugs or questions, [open an issue](https://github.com/openvax/varcode/issues).
+Contributions are welcome; see [CONTRIBUTING.md](CONTRIBUTING.md) and the
+[changelog](CHANGELOG.md).

{varcode-9.2.3 → varcode-9.2.5}/varcode.egg-info/SOURCES.txt

@@ -6,6 +6,7 @@ requirements.txt
 tests/test_annotator_divergence_scenarios.py
 tests/test_annotator_parity_adversarial.py
 tests/test_annotators.py
+tests/test_bnd_retained_segments.py
 tests/test_cli_effects.py
 tests/test_cli_genes.py
 tests/test_cli_without_pkg_resources.py
@@ -17,6 +18,7 @@ tests/test_cryptic_exons.py
 tests/test_csv_roundtrip.py
 tests/test_dbnsfp_validation.py
 tests/test_default_structural_helpers.py
+tests/test_documentation_examples.py
 tests/test_effect_annotation_errors.py
 tests/test_effect_candidates.py
 tests/test_effect_classes.py