16 lines
846 B
Python
16 lines
846 B
Python
from mlstmyfasta.engine.annotations import annotate_from_genbank, fetch_ncbi_genbank
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from Bio import SeqIO
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from mlstmyfasta.engine.data.genomics import AnnotatedString
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async def test_fetch_ncbi_genbank_with_id_works():
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assert len((await fetch_ncbi_genbank("CP011448.1")).sequence) > 0
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async def test_annotate_from_genbank_for_adk_annotation():
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sequence = SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq
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annotated_sequence = await annotate_from_genbank("CP011448.1", "bpertussis_tohamaI", str(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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