def subtype_heidelberg_pass():
return Subtype(scheme=scheme_heidelberg,
scheme_version=SCHEME_FASTAS[scheme_heidelberg]['version'],
sample=genome_name,
subtype='2.2.1.1.1.1',
file_path=fastq_heidelberg_pass,
are_subtypes_consistent=True,
n_tiles_matching_all=202,
n_tiles_matching_all_expected='202',
n_tiles_matching_positive=20,
n_tiles_matching_positive_expected='20',
n_tiles_matching_subtype=2,
n_tiles_matching_subtype_expected='2',
qc_status=QC.PASS)
def subtype_enteritidis_fail():
return Subtype(scheme=scheme_enteritidis,
scheme_version=SCHEME_FASTAS[scheme_enteritidis]['version'],
sample=genome_name,
subtype='2.2.4.1',
file_path=fastq_heidelberg_pass,
are_subtypes_consistent=False,
n_tiles_matching_all=182,
n_tiles_matching_all_expected='224',
n_tiles_matching_positive=22,
n_tiles_matching_positive_expected='21',
n_tiles_matching_subtype=5,
n_tiles_matching_subtype_expected='6',
qc_status=QC.FAIL)
def subtype_typhi_AE014613_pass():
return Subtype(scheme=scheme_typhi,
scheme_version=SCHEME_FASTAS[scheme_typhi]['version'],
sample=genome_name,
subtype='2.3.6.1',
file_path=fasta_typhi_pass,
are_subtypes_consistent=True,
n_kmers_matching_all=68,
n_kmers_matching_all_expected='68',
n_kmers_matching_positive=4,
n_kmers_matching_positive_expected='4',
n_kmers_matching_subtype=1,
n_kmers_matching_subtype_expected='1',
qc_status=QC.PASS)
def subtype_typhimurium_pass():
return Subtype(scheme=scheme_typhimurium,
scheme_version=SCHEME_FASTAS[scheme_typhimurium]['version'],
sample=genome_name,
subtype='2.2.3.3',
file_path=fasta_typhimurium_pass,
are_subtypes_consistent=True,
n_kmers_matching_all=429,
n_kmers_matching_all_expected='430',
n_kmers_matching_positive=19,
n_kmers_matching_positive_expected='19',
n_kmers_matching_subtype=5,
n_kmers_matching_subtype_expected='5',
qc_status=QC.PASS)
def subtype_enteritidis_fail():
return Subtype(scheme=scheme_enteritidis,
scheme_version=SCHEME_FASTAS[scheme_enteritidis]['version'],
sample=genome_name,
subtype='2.1.5.4',
file_path=fasta_enteritidis_fail,
are_subtypes_consistent=True,
n_kmers_matching_all=114,
n_kmers_matching_all_expected='317',
n_kmers_matching_positive=9,
n_kmers_matching_positive_expected='10',
n_kmers_matching_subtype=1,
n_kmers_matching_subtype_expected='1',
qc_status=QC.FAIL)
def subtype_tb_AP018036_pass():
return Subtype(
scheme=scheme_tuberculosis,
scheme_version=SCHEME_FASTAS[scheme_tuberculosis]['version'],
sample=genome_name,
subtype='2.2.1',
file_path=fasta_tb_pass,
are_subtypes_consistent=True,
n_kmers_matching_all=62,
n_kmers_matching_all_expected='62',
n_kmers_matching_positive=3,
n_kmers_matching_positive_expected='3',
n_kmers_matching_subtype=1,
n_kmers_matching_subtype_expected='1',
qc_status=QC.PASS)
def subtype_heidelberg_pass():
return Subtype(scheme=scheme_heidelberg,
scheme_version=SCHEME_FASTAS[scheme_heidelberg]['version'],
sample=genome_name,
file_path=fasta_heidelberg_pass,
subtype='2.2.2.2.1.4',
are_subtypes_consistent=True,
inconsistent_subtypes=None,
n_kmers_matching_all=202,
n_kmers_matching_all_expected='202',
n_kmers_matching_positive=17,
n_kmers_matching_positive_expected='17',
n_kmers_matching_subtype=3,
n_kmers_matching_subtype_expected='3',
qc_status=QC.PASS)
def test_empty_results():
st = Subtype(sample='test',
file_path='tests/data/Retro1000data/10-1358.fastq',
scheme='enteritidis',
scheme_version='0.8.0',
subtype=None,
non_present_subtypes=None,
all_subtypes=None,
qc_status=QC.FAIL,
qc_message=QC.NO_TARGETS_FOUND)
df_empty = empty_results(st)
df_expected_empty = pd.DataFrame({0: dict(sample='test',
file_path='tests/data/Retro1000data/10-1358.fastq',
subtype=None,
refposition=None,
is_pos_tile=None,
scheme='enteritidis',
scheme_version='0.8.0',
qc_status=QC.FAIL,
qc_message=QC.NO_TARGETS_FOUND)}).transpose()
assert ((df_empty == df_expected_empty) | (df_empty.isnull() == df_expected_empty.isnull())).values.all(), \
f'Empty result DataFrame should equal df_expected_empty: {df_expected_empty}'