16 lines
866 B
Python
16 lines
866 B
Python
from Bio import SeqIO
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from mlstmyfasta.engine.data.MLST import Allele
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from mlstmyfasta.engine.remote.databases.institutpasteur.profiling import InstitutPasteurProfiler
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async def test_profiling_results_in_exact_matches_when_exact():
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sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
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async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
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exact_matches = dummy_profiler.fetch_mlst_profile(sequence_string=sequence)
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targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
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async for exact_match in exact_matches:
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assert isinstance(exact_match, Allele)
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assert exact_match.allele_variant == '1' # All of Tohama I has allele id I
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targets_left.remove(exact_match.allele_loci)
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assert len(targets_left) == 0 |