def test_save():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
isolate = 'tests'
amr_obj.logger = logging.getLogger(__name__)
summary_drugs = pandas.DataFrame(
{
"Isolate": isolate,
'ESBL': 'blaCTX-M-15',
"Beta-lactamase (not ESBL or carbapenemase)": 'blaSHV-11'
},
index=[0])
summary_partial = pandas.DataFrame(
{
"Isolate": isolate,
'ESBL': 'blaCTX-M-15'
}, index=[0])
virulence = pandas.DataFrame({
"Isolate": isolate,
'METAL': 'qnrB1'
},
index=[0])
assert amr_obj.save_files('', summary_drugs, summary_partial,
virulence)
def test_get_per_isolate():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
reftab = pandas.read_csv(REFGENES)
reftab = reftab.fillna('-')
df = pandas.read_csv('tests/amrfinder.out', sep='\t')
isolate = 'tests'
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj.get_per_isolate(
reftab=reftab, df=df, isolate=isolate) == ({
"Isolate":
isolate,
"Beta-lactamase (not ESBL or carbapenemase)":
'blaSHV-11',
'ESBL':
'blaCTX-M-15'
}, {
"Isolate": isolate,
'ESBL': 'blaCTX-M-15'
}, {
"Isolate": isolate,
'Metal': 'qnrB1'
})
def run_pipeline(args):
P = SetupAMR(args)
input_data = P.setup()
A = RunFinder(input_data)
amr_data = A.run()
C = Collate(amr_data)
collated_data = C.run()
def test_extract_gene_name_1():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
reftab = pandas.read_csv(REFGENES)
protein = 'WP_004176269.1'
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj.extract_gene_name(protein, reftab) == 'blaSHV-11'
def test_extract_gene_name_2():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
reftab = pandas.read_csv(REFGENES)
reftab = reftab.fillna('-')
protein = 'WP_063839881.1'
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj.extract_gene_name(protein, reftab) == "aac(2')-IIa"
def test_save_merge_both_empty():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
isolate = 'tests'
amr_obj.logger = logging.getLogger(__name__)
summary_drugs = pandas.DataFrame({"Isolate": isolate}, index=[0])
summary_partial = pandas.DataFrame({"Isolate": isolate}, index=[0])
virulence = pandas.DataFrame()
assert not amr_obj._merge(summary_drugs, summary_partial).empty
def test_get_cols_empty():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
isolate = 'tests'
amr_obj.logger = logging.getLogger(__name__)
summary_drugs = pandas.DataFrame()
# summary_partial = pandas.DataFrame({"Isolate":isolate,'ESBL':'blaCTX-M-15'}, index = [0])
# virulence = pandas.DataFrame({"Isolate":isolate,'METAL':'qnrB1'}, index = [0])
assert amr_obj._get_cols(df=summary_drugs) == []
def test_commbine_all_empty():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
isolate = 'tests'
amr_obj.logger = logging.getLogger(__name__)
summary_drugs = pandas.DataFrame()
summary_partial = pandas.DataFrame()
virulence = pandas.DataFrame()
assert amr_obj._combine_dfs(summary_drugs, summary_partial,
virulence).empty
def test_get_drugclass_allele_1():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
reftab = pandas.read_csv(REFGENES)
df = pandas.read_csv('tests/amrfinder.out', sep='\t')
for i in df.iterrows():
if i[1]['Gene symbol'] == 'blaSHV-11':
row = i
colname = 'allele'
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj.get_drugclass(
reftab, row,
colname) == "Beta-lactamase (not ESBL or carbapenemase)"
def test_setup_dict():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
reftab = pandas.read_csv(REFGENES)
reftab = reftab.fillna('-')
drugclass_dict = {}
df = pandas.read_csv('tests/amrfinder.out', sep='\t')
for i in df.iterrows():
if i[1]['Gene symbol'] == 'blaSHV-11':
row = i
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj.setup_dict(drugclass_dict, reftab, row) == {
"Beta-lactamase (not ESBL or carbapenemase)": ['blaSHV-11']
}
def test_collate():
"""
assert True when non-empty string is given
"""
with patch.object(Collate, "__init__", lambda x: None):
args = Colls("assembly", 'tests/contigs.fa', '')
amr_obj = Collate()
reftab = pandas.read_csv(REFGENES)
reftab = reftab.fillna('-')
isolate = 'tests'
drugs = pandas.DataFrame(
{
"Isolate": isolate,
'ESBL': 'blaCTX-M-15',
"Beta-lactamase (not ESBL or carbapenemase)": 'blaSHV-11'
},
index=[0])
partial = pandas.DataFrame({
"Isolate": isolate,
'ESBL': 'blaCTX-M-15'
},
index=[0])
virulence = pandas.DataFrame({
"Isolate": isolate,
'Metal': 'qnrB1'
},
index=[0])
# print(drugs)
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj.collate(isolate)[0].equals(drugs)
assert amr_obj.collate(isolate)[1].equals(partial)
assert amr_obj.collate(isolate)[2].equals(virulence)