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Tested annotation alignment system

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This commit is contained in:
Harrison Deng
2025-01-03 14:39:18 +00:00
parent 28733337d2
commit b834aa93b0
9 changed files with 28 additions and 25 deletions
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tests/mlstmyfasta/engine/external/databases/institutpasteur/test_access.py vendored Normal file
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9
tests/mlstmyfasta/engine/test_annotations.py
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@@ -6,7 +6,10 @@ from mlstmyfasta.engine.data.genomics import AnnotatedString
async def test_fetch_ncbi_genbank_with_id_works():
assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0
async def test_annotate_from_genbank_results_in_annotations():
async def test_annotate_from_genbank_for_adk_annotation():
sequence = SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq
annotated_sequence = await annotate_from_genbank("CP011448.1", "bpertussis_tohamaI", str(sequence))
assert annotated_sequence is AnnotatedString
annotated_sequence = await annotate_from_genbank("CP011448.1", "bpertussis_tohamaI", str(sequence), max_annotation_length=750, gene_targets=set(["adk"]))
assert isinstance(annotated_sequence, AnnotatedString)
assert len(annotated_sequence.annotations) >= 1
assert annotated_sequence.annotations[0].type == "gene"
assert "adk" in annotated_sequence.annotations[0].feature_properties["gene"]