def test_check_query_for_input_column():
config = cfunk.get_defaults()
config["query"] = os.path.join(thisdir, "test.csv")
qcfunk.check_query_for_input_column(config)
test_query_header = "name,display,HCW_status,care_home,sample_date,date_2,date_3,adm2,test,test2,outer_postcode,x_col,y_col,adm1_blah".split(
",")
assert config["query_metadata_header"] == test_query_header
def test_generate_query_from_metadata():
config = cfunk.get_defaults()
config["background_metadata"] = os.path.join(thisdir,
"test_background.csv")
from_metadata = "adm2=Edinburgh sample_date=2020-10-01"
query = qcfunk.generate_query_from_metadata("test_from_metadata.csv",
from_metadata,
config["background_metadata"],
config)
c = 0
with open(query, "r") as f:
for l in f:
c += 1
assert c == 5
from_metadata = "adm2=Edinburgh sample_date=2020-10-01:2020-10-10"
query = qcfunk.generate_query_from_metadata("test_from_metadata.csv",
from_metadata,
config["background_metadata"],
config)
c = 0
with open(query, "r") as f:
for l in f:
c += 1
assert c == 12
def test_background_metadata_header():
config = cfunk.get_defaults()
config["background_metadata"] = os.path.join(thisdir,
"test_background.csv")
test_header = "central_sample_id,biosample_source_id,sequence_name,secondary_identifier,sample_date,epi_week,country,adm1,is_surveillance,is_community,is_hcw,is_travel_history,travel_history,lineage,lineage_support,uk_lineage,acc_lineage,del_lineage,phylotype,adm2".split(
",")
qcfunk.check_metadata_for_search_columns(config)
assert test_header == config["background_metadata_header"]
def test_max_ambig():
config = cfunk.get_defaults()
print(cwd)
config["query"] = os.path.join(thisdir, "test.csv")
config["fasta"] = os.path.join(thisdir, "test.fasta")
config["outdir"] = thisdir
config["background_metadata"] = os.path.join(thisdir,
"test_background.csv")
num_seqs = qcfunk.input_file_qc(None, 0, config)
assert num_seqs == 2
def test_configure_update():
config = cfunk.get_defaults()
config["from_metadata"] = "sample_date=2020-10-04"
cfunk.configure_update(True, config)
assert config["colour_by"] == "new:Paired"
assert config["tree_fields"] == "new"
assert config[
"table_fields"] == "central_sample_id,sequence_name,sample_date,uk_lineage,phylotype,tree,new"
assert config["tempdir"] == ""
assert config["outdir"] == ""
def test_map_sequences_config():
config = cfunk.get_defaults()
config["background_metadata"] = os.path.join(thisdir,
"test_background.csv")
qcfunk.check_metadata_for_search_columns(config)
config[
"query_metadata_header"] = "name,display,HCW_status,care_home,sample_date,date_2,date_3,adm2,test,test2,outer_postcode,x_col,y_col,adm1_blah".split(
",")
config["map_info"] = "outer_postcode"
config["map_sequences"] = True
cfunk.map_sequences_config(config)
assert config["input_crs"] == "EPSG:4326"
def test_get_sequencing_centre_header():
config = cfunk.get_defaults()
qcfunk.get_outdir(None, None, cwd, config)
config["sequencing_centre"] = "EDIN"
cfunk.get_sequencing_centre_header(config)
assert config["sequencing_centre_file"] == "./figures/EDIN.png"
def test_configure_cluster():
config = cfunk.get_defaults()
cfunk.configure_cluster(config)
assert config["down_distance"] == 100
def test_outdir_and_prefix():
config = cfunk.get_defaults()
qcfunk.get_outdir("outdir_arg", "prefix", cwd, config)
outdir = config["outdir"].split("/")[-1]
assert outdir.startswith("outdir_arg")
def test_outdir_arg():
config = cfunk.get_defaults()
qcfunk.get_outdir("input_arg", None, cwd, config)
outdir = config["outdir"].split("/")[-1]
assert outdir.startswith("input_arg")
def test_outdir_default():
config = cfunk.get_defaults()
qcfunk.get_outdir(None, None, cwd, config)
outdir = config["outdir"].split("/")[-1]
assert outdir.startswith("civet")