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Merge branch 'features/improved-oop-architecture' into features/non-exact-notation

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README.md
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@ -1,6 +1,6 @@
# autoBIGS.Engine # autoBIGS.Engine
A python library implementing common BIGSdb MLST schemes and databases. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`. A python library implementing common BIGSdb MLST schemes and databases accesses for the purpose of typing sequences automatically. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`.
## Features ## Features

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tests/autobigs/engine/analysis/test_bigsdb.py
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@ -50,17 +50,17 @@ bpertussis_tohamaI_bad_profile = MLSTProfile((
Allele("pgm", "5", None), Allele("pgm", "5", None),
), "unknown", "unknown") ), "unknown", "unknown")
hinfluenzae_fdaargos_profile = MLSTProfile(( hinfluenzae_2014_102_profile = MLSTProfile((
Allele("adk", "1", None), Allele("adk", "28", None),
Allele("atpG", "1", None), Allele("atpG", "33", None),
Allele("frdB", "1", None), Allele("frdB", "7", None),
Allele("fucK", "1", None), Allele("fucK", "18", None),
Allele("mdh", "1", None), Allele("mdh", "11", None),
Allele("pgi", "1", None), Allele("pgi", "125", None),
Allele("recA", "5", None) Allele("recA", "89", None)
), "3", "ST-3 complex") ), "478", "unknown")
hinfluenzae_fdaargos_bad_profile = MLSTProfile(( hinfluenzae_2014_102_bad_profile = MLSTProfile((
Allele("adk", "3", None), Allele("adk", "3", None),
Allele("atpG", "121", None), Allele("atpG", "121", None),
Allele("frdB", "6", None), Allele("frdB", "6", None),
@ -68,15 +68,12 @@ hinfluenzae_fdaargos_bad_profile = MLSTProfile((
Allele("mdh", "12", None), Allele("mdh", "12", None),
Allele("pgi", "4", None), Allele("pgi", "4", None),
Allele("recA", "5", None) Allele("recA", "5", None)
), "3", "ST-3 complex") ), "unknown", "unknown")
hinfluenzae_fdaargos_sequence = str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza.fasta", "fasta").seq)
hinfluenzae_fdaargos_fragmented_sequence = tuple(SeqIO.parse("tests/resources/tohama_I_bpertussis_features.fasta", "fasta"))
@pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [ @pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [
(False, "https://bigsdb.pasteur.fr/api", "pubmlst_bordetella_seqdef", 3, "tohama_I_bpertussis.fasta", "tohama_I_bpertussis_features.fasta", bpertussis_tohamaI_profile, bpertussis_tohamaI_bad_profile), (False, "https://bigsdb.pasteur.fr/api", "pubmlst_bordetella_seqdef", 3, "tohama_I_bpertussis.fasta", "tohama_I_bpertussis_features.fasta", bpertussis_tohamaI_profile, bpertussis_tohamaI_bad_profile),
(False, "https://rest.pubmlst.org", "pubmlst_hinfluenzae_seqdef", 1, "fdaargos_1560_hinfluenza.fasta", "fdaargos_1560_hinfluenza_features.fasta", hinfluenzae_fdaargos_profile, hinfluenzae_fdaargos_bad_profile), (False, "https://rest.pubmlst.org", "pubmlst_hinfluenzae_seqdef", 1, "2014-102_hinfluenza.fasta", "2014-102_hinfluenza_features.fasta", hinfluenzae_2014_102_profile, hinfluenzae_2014_102_bad_profile),
]) ])
class TestBIGSdbMLSTProfiler: class TestBIGSdbMLSTProfiler:
async def test_profiling_results_in_exact_matches_when_exact(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile): async def test_profiling_results_in_exact_matches_when_exact(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
@ -202,7 +199,6 @@ class TestBIGSdbIndex:
assert databases["pubmlst_bordetella_seqdef"] == "https://bigsdb.pasteur.fr/api" assert databases["pubmlst_bordetella_seqdef"] == "https://bigsdb.pasteur.fr/api"
@pytest.mark.parametrize("local", [ @pytest.mark.parametrize("local", [
(True),
(False) (False)
]) ])
async def test_bigsdb_index_instantiates_correct_profiler(self, local): async def test_bigsdb_index_instantiates_correct_profiler(self, local):

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tests/resources/fdaargos_1560_hinfluenza.fasta
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tests/resources/fdaargos_1560_hinfluenza_adk.fasta
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>lcl|CP085952.1_gene_371 [gene=adk] [locus_tag=LK401_01855] [location=complement(365128..365772)] [gbkey=Gene]
ATGAAAATTATTCTTTTAGGTGCACCGGGTGCAGGTAAAGGCACTCAAGCACAATTTATTATGAACAAAT
TTGGTATCCCGCAAATTTCAACTGGTGATATGTTCCGTGCTGCAATCAAAGCGGGGACTGAACTTGGCAA
ACAAGCTAAAGCATTAATGGATGAAGGTAAATTAGTGCCAGATGAATTAACCGTTGCCCTTGTAAAAGAT
CGTATTGCTCAAGCTGACTGCACAAATGGTTTCTTGTTAGATGGTTTCCCTCGTACTATTCCACAAGCGG
ATGCACTGAAAGATTCAGGTGTTAAAATTGACTTTGTTTTAGAATTTGATGTGCCAGACGAAGTGATTGT
TGAACGTATGAGTGGCCGTCGCGTACACCAAGCGTCTGGCCGTTCTTACCACATCGTTTATAATCCACCA
AAAGTGGAAGGTAAAGATGATGTAACAGGCGAAGATTTAATTATTCGTGCAGACGATAAACCAGAAACTG
TATTAGATCGTTTAGCCGTATATCATAAACAAACTAGCCCATTAATTGATTATTACCAAGCAGAAGCGAA
AGCGGGGAATACTCAATATTTCCGTTTAGACGGTACACAAAAAGTAGAAGAAGTTAGCCAAGAGTTAGAT
AAAATCTTAGGCTAA

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tests/resources/fdaargos_1560_hinfluenza_features.fasta
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