orfdata 0.32.0__tar.gz → 0.33.0__tar.gz

{orfdata-0.32.0/orfdata.egg-info → orfdata-0.33.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.32.0
+Version: 0.33.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -113,11 +113,15 @@ Human evidence is never transferred to another species. Viral proteomes can be a
 orfdata also provides [RNA, ribosome and protein measurements](https://openvax.github.io/orfdata/measurements/)
 for human, mouse, dog and yeast.
 
-`viral_orfs(reference_dna, contig="HPV16")` loads source-defined viral CDSs as
-existing RNA/ORF models, offline and qualified by exact reference sequence.
+`viral_references(host="human", group="HPV", virus_type="HPV16")` finds the
+source-qualified viral references. `viral_reference_sequence(id)` supplies the
+packaged bases, and `viral_orfs(reference_id=id)` loads their coding paths.
+When annotating an existing alignment, `viral_orfs(reference_dna,
+contig="HPV16")` checks its actual reference sequence before applying the same
+models.
 The first [coding reference](https://openvax.github.io/orfdata/viral/) contains
 the nine RefSeq NC_001526.4 HPV16 CDSs, with native and GDC placements;
-`viral_references()` lists the available identities and coverage. Broader
+the host association is distinct from the virus's own taxon. Broader
 imports remain in [the viral roadmap](https://github.com/openvax/orfdata/issues/91).
 
 ## Measurement datasets

{orfdata-0.32.0 → orfdata-0.33.0}/README.md

@@ -81,11 +81,15 @@ Human evidence is never transferred to another species. Viral proteomes can be a
 orfdata also provides [RNA, ribosome and protein measurements](https://openvax.github.io/orfdata/measurements/)
 for human, mouse, dog and yeast.
 
-`viral_orfs(reference_dna, contig="HPV16")` loads source-defined viral CDSs as
-existing RNA/ORF models, offline and qualified by exact reference sequence.
+`viral_references(host="human", group="HPV", virus_type="HPV16")` finds the
+source-qualified viral references. `viral_reference_sequence(id)` supplies the
+packaged bases, and `viral_orfs(reference_id=id)` loads their coding paths.
+When annotating an existing alignment, `viral_orfs(reference_dna,
+contig="HPV16")` checks its actual reference sequence before applying the same
+models.
 The first [coding reference](https://openvax.github.io/orfdata/viral/) contains
 the nine RefSeq NC_001526.4 HPV16 CDSs, with native and GDC placements;
-`viral_references()` lists the available identities and coverage. Broader
+the host association is distinct from the virus's own taxon. Broader
 imports remain in [the viral roadmap](https://github.com/openvax/orfdata/issues/91).
 
 ## Measurement datasets

orfdata-0.33.0/docs/viral.md

@@ -0,0 +1,72 @@
+# Viral coding references
+
+Browse the packaged viral references by host, convenience group and virus type,
+then load their source-annotated coding paths without fetching the genome:
+
+```python
+from orfdata import viral_orfs, viral_reference_sequence, viral_references
+
+references = viral_references(host="human", group="HPV", virus_type="HPV16")
+print([(r["id"], r["coding_models"]) for r in references])
+# [('NC_001526.4', 9), ('GRCh38.d1.vd1:HPV16', 9)]
+
+reference_dna = viral_reference_sequence("NC_001526.4")
+orfs = viral_orfs(reference_id="NC_001526.4")
+for orf in orfs:
+    print(orf.orf_id, orf.gene_name, orf.coding_blocks, orf.protein_sequence)
+```
+
+The small bundled catalogue loads offline without PyEnsembl, Biopython or a
+human genome. It supplies the complete DNA for the native RefSeq NC_001526.4
+and GDC HPV16 placements; both map to the same nine source CDSs. The two DNA
+strings differ by a verified circular rotation. `viral_reference_sequence(id)`
+returns the exact forward FASTA bases, with T rather than U. A missing ID raises
+`ValueError`. The metadata query does not copy genome bases into each result.
+
+`host` accepts a known species name such as `"human"` or an NCBI taxon ID such
+as `9606`. The released HPV16 reference records have viral `taxon_id=333760`
+and `host_taxon_ids=[9606]`; these are different identities. Their documented
+human host association is sourced to PaVE. `row["virus"]["group"] == "HPV"`
+is a convenient selection label, not a formal taxonomic rank. The
+`row["virus"]["type"] == "HPV16"` label is the virus
+type; ICTV places it in the species *Alphapapillomavirus 9*. Each row also
+retains the association and taxonomy source URLs. Host associations can cover
+several host taxa as new references are curated; an unlisted host is unknown,
+not proof that infection is impossible. NCBI Virus's isolation-host metadata is
+not an exhaustive host-range list. `host_taxon_ids` and `host_source` have the
+same meaning as in [ViralProteome](proteome.md#viral-proteomes).
+
+When annotating an existing BAM, continue to bind against its **actual** full
+alignment-reference DNA:
+
+```python
+orfs = viral_orfs(alignment_reference_dna, contig="HPV16")
+```
+
+This checks the sequence hash and its qualified coordinates. A contig name or
+related strain cannot transfer CDS annotations to mismatching DNA. It raises
+`ValueError` for an unavailable reference rather than returning an empty ORF
+set. `viral_references()` reports coverage and source checksums, and
+`viral_orfs()` returns the existing `SourceRNA`/`TranscriptORF` models.
+
+Each model uses a `SourceRNA` containing only the available CDS, including
+ordered splice blocks. Full transcript ends are not asserted. The existing
+`TranscriptORF.at()` validates its source protein and coding boundaries.
+These models have `orf_type="reference_CDS"`. Their internal kind `extra_orf`
+describes a source-defined ORF outside a loaded PyEnsembl annotation, not a
+claim that a RefSeq CDS is biologically noncanonical. No Ribo-seq or MS
+support is inferred from the reference annotation.
+
+The nine annotations are not an exhaustive HPV16 ORF catalogue. Other HPV
+types/lineages, EBV/KSHV, CMV, hepatitis viruses including HDV, HTLV-1/HIV,
+and polyomaviruses remain explicit coverage work in
+[issues #91–98](https://github.com/openvax/orfdata/issues/91).
+
+Isovar owns reconstructed sample RNA and read evidence. It can use these
+coding paths to anchor a frame on observed sequence, preserving variants
+and incomplete starts/stops. ORFdata does not assemble sample RNA, replace
+missing bases, infer protein abundance or establish viral tumor causality.
+RNA and coding-reference matches are not direct protein evidence.
+
+Source attribution and rebuilding instructions are in
+[`orfdata/data/viral/NOTICE.md`](https://github.com/openvax/orfdata/blob/main/orfdata/data/viral/NOTICE.md).

{orfdata-0.32.0 → orfdata-0.33.0}/orfdata/__init__.py

@@ -70,10 +70,11 @@ from .rna import IRES, ProteinProduct, RNAFeature, SourceRNA, products_from_unip
 from .search_reference import SearchMembership, SearchReference, SearchReferenceSpec, SearchSequence
 from .sequence import GeneticCode, genetic_code
 from .version import __version__
-from .viral import viral_orfs, viral_references
+from .viral import viral_orfs, viral_reference_sequence, viral_references
 
 __all__ = [
     "viral_orfs",
+    "viral_reference_sequence",
     "viral_references",
     "__version__",
     "Proteome",

{orfdata-0.32.0 → orfdata-0.33.0}/orfdata/data/viral/NOTICE.md

@@ -13,6 +13,17 @@ The catalogue contains nine source-annotated CDSs, including two joined paths.
 It does not claim all reported HPV16 ORFs or complete transcript models.
 RNA support does not establish translation or protein expression.
 
+The released catalogue also contains the full forward reference bases for both
+qualified placements. HPV16's documented human host is sourced from PaVE's
+HPV16REF record (`/host="Human (Homo sapiens)"`):
+https://pave.niaid.nih.gov/locus_viewer?feature_id=HPV16_E7&seq_id=HPV16REF .
+This host association applies to HPV16 as a type, not to all papillomaviruses,
+and does not claim an exhaustive host range. ICTV lists HPV16 in the species
+*Alphapapillomavirus 9*:
+https://ictv.global/report/chapter/papillomaviridae/taxonomy/papillomaviridae .
+These are distinct from the RefSeq DNA/CDS source and the GDC coordinate
+placement. Consulted 2026-10-16.
+
 Native DNA MD5: `08d2b3849496d12cc45fd4df713d5c2f`.
 GDC GRCh38.d1.vd1 HPV16 DNA MD5: `f2463721818c29998ef5ab917e6df74a`.
 GDC DNA is the source circle rotated by 864 bases. Both placements retain

orfdata-0.33.0/orfdata/version.py

@@ -0,0 +1 @@
+__version__ = "0.33.0"

{orfdata-0.32.0 → orfdata-0.33.0}/orfdata/viral.py

@@ -8,10 +8,10 @@ from functools import lru_cache
 from importlib.resources import files
 
 from .model import TranscriptORF
-from .reference import ReferenceContext
+from .reference import ReferenceContext, species_taxon
 from .rna import SourceRNA
 
-_CATALOG_SHA256 = "52ab8181b9d3f199dde3afabc8440ee9a8c912291c6425c99fb4225e29ad1a70"
+_CATALOG_SHA256 = "aca0c72948d4cda896d14b32203981bce4759e0c70212c05dca6f3d0e16ed4b4"
 _COMPLEMENT = str.maketrans("ACGT", "TGCA")
 
 
@@ -21,39 +21,84 @@ def _catalog():
     if hashlib.sha256(raw).hexdigest() != _CATALOG_SHA256:
         raise ValueError("Bundled viral CDS catalogue checksum mismatch")
     data = json.loads(gzip.decompress(raw))
-    if data["schema"] != "orfdata.viral_cds.v1":
+    if data["schema"] != "orfdata.viral_cds.v2":
         raise ValueError("Unsupported viral CDS catalogue schema")
     return data
 
 
-def viral_references():
-    """List released viral coding-reference identities, without network access.
+def viral_references(*, host=None, group=None, virus_type=None):
+    """Find released viral references by documented host, group and type.
+
+    Parameters
+    ----------
+    host : str or int, optional
+        Known host name such as ``"human"``, or an NCBI host taxon ID. A host
+        association is source-attributed and is not a complete host range.
+    group : str, optional
+        Convenience group label, such as ``"HPV"``; not a taxonomy rank.
+    virus_type : str, optional
+        Named virus type, such as ``"HPV16"``; distinct from ICTV species.
 
     Returns
     -------
     tuple of dict
-        Exact sequence hashes, accession/source pins, coding-model counts and
-        coverage scope. A listed reference is not a complete transcript or
-        exhaustive ORF catalogue. Returned dictionaries are independent copies.
+        Exact sequence hashes, source/host pins, virus identity and coverage.
+        A listed reference is not a complete transcript or exhaustive ORF
+        catalogue. Returned dictionaries are independent copies.
     """
+    if host is None:
+        host_taxon_id = None
+    elif type(host) is int and host > 0:
+        host_taxon_id = host
+    elif isinstance(host, str) and species_taxon(host) is not None:
+        host_taxon_id = species_taxon(host)
+    else:
+        raise ValueError("host must be a known species name or positive NCBI taxon ID")
+    if any(value is not None and (not isinstance(value, str) or not value)
+           for value in (group, virus_type)):
+        raise ValueError("group and virus_type must be nonempty names")
     data = _catalog()
     return tuple(dict(**{key: copy.deepcopy(value) for key, value in row.items()
-                         if key != "coding_blocks"},
+                         if key not in ("coding_blocks", "reference_sequence")},
                       coding_models=len(row["coding_blocks"]), scope=data["scope"],
                       catalogue_sha256=_CATALOG_SHA256,
                       products=[dict(protein_id=cds["protein_id"], gene=cds["gene"],
                                      product=cds["product"]) for cds in data["cds"]])
-                 for row in data["references"])
+                 for row in data["references"]
+                 if (host_taxon_id is None or host_taxon_id in row["host_taxon_ids"])
+                 and (group is None or row["virus"]["group"].casefold() == group.casefold())
+                 and (virus_type is None or row["virus"]["type"].casefold() == virus_type.casefold()))
+
+
+def viral_reference_sequence(reference_id):
+    """Return bundled, checksum-verified reference bases for one exact ID.
+
+    The sequence uses the forward FASTA alphabet (T rather than U) and may
+    represent a virus whose biological genome is RNA. No network is accessed.
+    """
+    matches = [row for row in _catalog()["references"] if row["id"] == reference_id]
+    if len(matches) != 1:
+        raise ValueError("No unique released viral reference ID matches this name")
+    row = matches[0]
+    sequence = row["reference_sequence"]
+    if (len(sequence) != row["length"] or
+            hashlib.sha256(sequence.encode("ascii")).hexdigest() != row["sequence_sha256"]):
+        raise ValueError("Bundled viral reference sequence checksum mismatch")
+    return sequence
 
 
-def viral_orfs(reference_sequence, *, contig=None):
+def viral_orfs(reference_sequence=None, *, reference_id=None, contig=None):
     """Load source-defined CDSs for one exactly matching viral DNA reference.
 
     Parameters
     ----------
-    reference_sequence : str
-        Complete forward reference DNA, not sample RNA. No annotation is
-        transferred to mismatching strains or by contig name alone.
+    reference_sequence : str, optional
+        Complete forward reference DNA from an alignment. This checks actual
+        sequence identity rather than transferring annotation by contig name.
+    reference_id : str, optional
+        Bundled reference ID from ``viral_references()``. Use this to load the
+        reference ORFs without obtaining DNA separately. Supply exactly one
+        of ``reference_sequence`` or ``reference_id``.
     contig : str, optional
         The caller's name for this exact DNA in an alignment reference. The
         original versioned source identity remains on every ORF's context.
@@ -72,7 +117,10 @@ def viral_orfs(reference_sequence, *, contig=None):
         No released coding reference matches, or a source model fails to bind
         and translate exactly. Discovery is available through viral_references.
     """
-    sequence = str(reference_sequence).upper()
+    if (reference_sequence is None) == (reference_id is None):
+        raise ValueError("Provide exactly one of reference_sequence or reference_id")
+    sequence = (viral_reference_sequence(reference_id) if reference_id is not None
+                else str(reference_sequence).upper())
     fingerprint = hashlib.sha256(sequence.encode("ascii")).hexdigest()
     data = _catalog()
     matches = [row for row in data["references"] if row["sequence_sha256"] == fingerprint

{orfdata-0.32.0 → orfdata-0.33.0/orfdata.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: orfdata
-Version: 0.32.0
+Version: 0.33.0
 Summary: Reference proteomes with evidence-backed noncanonical ORFs on PyEnsembl genomes
 Author: OpenVax
 License-Expression: Apache-2.0
@@ -113,11 +113,15 @@ Human evidence is never transferred to another species. Viral proteomes can be a
 orfdata also provides [RNA, ribosome and protein measurements](https://openvax.github.io/orfdata/measurements/)
 for human, mouse, dog and yeast.
 
-`viral_orfs(reference_dna, contig="HPV16")` loads source-defined viral CDSs as
-existing RNA/ORF models, offline and qualified by exact reference sequence.
+`viral_references(host="human", group="HPV", virus_type="HPV16")` finds the
+source-qualified viral references. `viral_reference_sequence(id)` supplies the
+packaged bases, and `viral_orfs(reference_id=id)` loads their coding paths.
+When annotating an existing alignment, `viral_orfs(reference_dna,
+contig="HPV16")` checks its actual reference sequence before applying the same
+models.
 The first [coding reference](https://openvax.github.io/orfdata/viral/) contains
 the nine RefSeq NC_001526.4 HPV16 CDSs, with native and GDC placements;
-`viral_references()` lists the available identities and coverage. Broader
+the host association is distinct from the virus's own taxon. Broader
 imports remain in [the viral roadmap](https://github.com/openvax/orfdata/issues/91).
 
 ## Measurement datasets

{orfdata-0.32.0 → orfdata-0.33.0}/tests/test_viral.py

@@ -4,13 +4,15 @@ import gzip
 import hashlib
 import io
 import json
+from copy import deepcopy
 from importlib.resources import files
 from pathlib import Path
 
 import pytest
 from Bio import SeqIO
 
-from orfdata import SourceRNA, viral_orfs, viral_references
+import orfdata.viral as viral_module
+from orfdata import SourceRNA, viral_orfs, viral_reference_sequence, viral_references
 from tools.build_hpv16_cds import build
 
 FIXTURE = Path(__file__).parent / "data/viral/NC_001526.4.gb.gz"
@@ -86,11 +88,66 @@ def test_discovery_is_offline_and_returned_metadata_cannot_change_loading(source
     assert {row["id"] for row in references} == {"NC_001526.4", "GRCh38.d1.vd1:HPV16"}
     assert all(row["coding_models"] == 9 for row in references)
     assert all(row["catalogue_sha256"] and row["source"]["sha256"] for row in references)
+    assert all("reference_sequence" not in row for row in references)
     references[0]["source"]["accession"] = "changed"
+    references[0]["host_taxon_ids"].clear()
     assert viral_references()[0]["source"]["accession"] == "NC_001526.4"
+    assert viral_references()[0]["host_taxon_ids"] == [9606]
     assert viral_orfs(str(record.seq))[0].context.annotation_version == "NC_001526.4"
 
 
+def test_host_group_and_type_select_exact_references_with_distinct_taxa():
+    references = viral_references(host="human", group="HPV", virus_type="HPV16")
+    assert {row["id"] for row in references} == {"NC_001526.4", "GRCh38.d1.vd1:HPV16"}
+    assert viral_references(host=9606, group="hpv", virus_type="hpv16") == references
+    assert viral_references(host="mouse") == viral_references(host=10090) == ()
+    assert viral_references(host="human", virus_type="HPV18") == ()
+    for row in references:
+        assert row["taxon_id"] == 333760 and row["host_taxon_ids"] == [9606]
+        assert "PaVE HPV16REF" in row["host_source"]
+        assert row["virus"]["ictv_species"] == "Alphapapillomavirus 9"
+        assert row["virus"]["group"] == "HPV" and row["virus"]["type"] == "HPV16"
+        assert row["virus"]["taxonomy_source"].startswith("https://ictv.global/")
+    for invalid in ("not_a_host", 0, True):
+        with pytest.raises(ValueError, match="host"):
+            viral_references(host=invalid)
+
+
+def test_explicit_multiple_host_associations_can_select_one_reference_from_each_host(monkeypatch):
+    # Synthetic metadata checks selection only; it makes no HPV16 mouse-host claim.
+    catalog = deepcopy(viral_module._catalog())
+    catalog["references"][0]["host_taxon_ids"].append(10090)
+    catalog["references"][0]["host_source"] = "synthetic multiple-host fixture"
+    monkeypatch.setattr(viral_module, "_catalog", lambda: catalog)
+    assert {row["id"] for row in viral_references(host="human")} == {
+        "NC_001526.4", "GRCh38.d1.vd1:HPV16"}
+    mouse, = viral_references(host="mouse", virus_type="HPV16")
+    assert mouse["id"] == "NC_001526.4" and mouse["taxon_id"] == 333760
+
+
+def test_bundled_reference_sequences_and_named_orfs_match_both_source_placements(source):
+    _, record = source
+    native = str(record.seq)
+    gdc = native[-864:] + native[:-864]
+    for reference_id, expected in (("NC_001526.4", native),
+                                   ("GRCh38.d1.vd1:HPV16", gdc)):
+        sequence = viral_reference_sequence(reference_id)
+        assert sequence == expected
+        row, = (r for r in viral_references() if r["id"] == reference_id)
+        assert hashlib.sha256(sequence.encode()).hexdigest() == row["sequence_sha256"]
+        by_name = viral_orfs(reference_id=reference_id, contig="selected")
+        by_dna = viral_orfs(sequence, contig="selected")
+        assert [(o.orf_id, o.coding_blocks, o.protein_sequence) for o in by_name] == [
+            (o.orf_id, o.coding_blocks, o.protein_sequence) for o in by_dna]
+        assert {o.transcript.contig for o in by_name} == {"selected"}
+    with pytest.raises(ValueError, match="reference ID"):
+        viral_reference_sequence("unknown")
+    with pytest.raises(ValueError, match="exactly one"):
+        viral_orfs()
+    with pytest.raises(ValueError, match="exactly one"):
+        viral_orfs(native, reference_id="NC_001526.4")
+
+
 def test_corrupt_packaged_catalogue_fails_before_returning_models(monkeypatch):
     import orfdata.viral as module
 

{orfdata-0.32.0 → orfdata-0.33.0}/tools/build_hpv16_cds.py

@@ -20,6 +20,9 @@ GDC_MD5 = "f2463721818c29998ef5ab917e6df74a"
 ROTATION = 864
 SOURCE = ("https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?"
           "id=NC_001526.4&db=nuccore&report=genbank&retmode=text")
+HOST_SOURCE = ("PaVE HPV16REF /host=Human (Homo sapiens), checked 2026-10-16: "
+               "https://pave.niaid.nih.gov/locus_viewer?feature_id=HPV16_E7&seq_id=HPV16REF")
+TAXONOMY_SOURCE = "https://ictv.global/report/chapter/papillomaviridae/taxonomy/papillomaviridae"
 
 
 def build(genbank):
@@ -65,8 +68,11 @@ def build(genbank):
         references.append(dict(id=name, taxon_id=333760, species="human_papillomavirus_16",
             length=len(sequence), sequence_md5=hashlib.md5(sequence.encode()).hexdigest(),
             sequence_sha256=hashlib.sha256(sequence.encode()).hexdigest(),
-            source=source, native_to_reference_rotation=offset, coding_blocks=blocks))
-    return dict(schema="orfdata.viral_cds.v1", source=source,
+            source=source, native_to_reference_rotation=offset, coding_blocks=blocks,
+            reference_sequence=sequence, host_taxon_ids=[9606], host_source=HOST_SOURCE,
+            virus=dict(group="HPV", type="HPV16", ictv_species="Alphapapillomavirus 9",
+                       taxonomy_source=TAXONOMY_SOURCE)))
+    return dict(schema="orfdata.viral_cds.v2", source=source,
                 scope="Nine source-annotated HPV16 CDSs; not all HPV ORFs or complete transcript models",
                 references=references, cds=definitions)
 

orfdata-0.32.0/docs/viral.md

@@ -1,45 +0,0 @@
-# Viral coding references
-
-`viral_orfs()` returns existing `TranscriptORF` objects for source-annotated
-viral CDSs. Supply the complete reference DNA that the RNA was aligned to:
-
-```python
-from orfdata import viral_orfs, viral_references
-
-print([(r["id"], r["coding_models"]) for r in viral_references()])
-# [('NC_001526.4', 9), ('GRCh38.d1.vd1:HPV16', 9)]
-
-orfs = viral_orfs(reference_dna, contig="HPV16")
-for orf in orfs:
-    print(orf.orf_id, orf.gene_name, orf.coding_blocks, orf.protein_sequence)
-```
-
-The small bundled catalogue loads offline without PyEnsembl, Biopython or a
-human genome. Its nine HPV16 CDSs come from RefSeq NC_001526.4. The loader
-requires an exact full-DNA hash and separately qualifies native and GDC
-circular rotations. A contig name or related strain is insufficient.
-An unavailable reference raises `ValueError`, distinct from a valid empty query.
-`viral_references()` exposes exact identities, coding coverage, source pins
-and product names without loading other data.
-
-Each model uses a `SourceRNA` containing only the available CDS, including
-ordered splice blocks. Full transcript ends are not asserted. The existing
-`TranscriptORF.at()` validates its source protein and coding boundaries.
-These models have `orf_type="reference_CDS"`. Their internal kind `extra_orf`
-describes a source-defined ORF outside a loaded PyEnsembl annotation, not a
-claim that a RefSeq CDS is biologically noncanonical. No Ribo-seq or MS
-support is inferred from the reference annotation.
-
-The nine annotations are not an exhaustive HPV16 ORF catalogue. Other HPV
-types/lineages, EBV/KSHV, CMV, hepatitis viruses including HDV, HTLV-1/HIV,
-and polyomaviruses remain explicit coverage work in
-[issues #91–98](https://github.com/openvax/orfdata/issues/91).
-
-Isovar owns reconstructed sample RNA and read evidence. It can use these
-coding paths to anchor a frame on observed sequence, preserving variants
-and incomplete starts/stops. ORFdata does not assemble sample RNA, replace
-missing bases, infer protein abundance or establish viral tumor causality.
-RNA and coding-reference matches are not direct protein evidence.
-
-Source attribution and rebuilding instructions are in
-[`orfdata/data/viral/NOTICE.md`](https://github.com/openvax/orfdata/blob/main/orfdata/data/viral/NOTICE.md).

orfdata-0.32.0/orfdata/version.py

@@ -1 +0,0 @@
-__version__ = "0.32.0"