13 lines
714 B
Python
13 lines
714 B
Python
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from automlst.engine.annotate import annotate_from_genbank, fetch_ncbi_genbank
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from Bio import SeqIO
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from automlst.engine.data.genomics import AnnotatedString
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async def test_annotate_from_genbank_for_adk_annotation():
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sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
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annotated_sequence = await annotate_from_genbank("CP011448.1", "bpertussis_tohamaI", sequence, max_annotation_length=750, gene_targets=set(["adk"]))
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assert isinstance(annotated_sequence, AnnotatedString)
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assert len(annotated_sequence.annotations) >= 1
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assert annotated_sequence.annotations[0].type == "gene"
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assert "adk" in annotated_sequence.annotations[0].feature_properties["gene"]
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