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import Bio.SeqIO
import Bio.Seq
from pathlib import Path
import sys
# make sure we get the local version of parse
sys.path.insert(0, (str(Path(__file__).parent.parent.parent)))
from augur import parse
class TestParse:
def test_fix_dates(self, capsys):
full_date = "4-5-2020"
assert parse.fix_dates(full_date) == "2020-05-04"
assert parse.fix_dates(full_date, dayfirst=False) == "2020-04-05"
partial_date_no_month = "2020-04"
assert parse.fix_dates(partial_date_no_month) == "2020-04-XX"
assert parse.fix_dates(partial_date_no_month, dayfirst=False) == "2020-04-XX"
partial_date_only_year = "2020"
assert parse.fix_dates(partial_date_only_year) == "2020-XX-XX"
# We should allow valid ambiguous dates to pass through the function
# without a warning to the user.
valid_ambiguous_date = "2020-XX-XX"
assert parse.fix_dates(valid_ambiguous_date) == valid_ambiguous_date
assert "WARNING" not in capsys.readouterr().err
# We should warn the user when their dates cannot be parsed by pandas or
# as a valid ambiguous date.
malformed_date = "Aaasd123AS"
assert(parse.fix_dates(malformed_date)) == malformed_date
assert "WARNING" in capsys.readouterr().err
def test_prettify(self):
# test trim
trim_string = "trim_here"
assert parse.prettify(trim_string, trim=4) == trim_string[:4] + "..."
trim_string_short = "trim"
assert parse.prettify(trim_string_short, trim=4) == trim_string_short
# test caps
caps_string_pos = "usa"
caps_string_neg = "usad"
assert parse.prettify(caps_string_pos) == caps_string_pos.upper()
assert parse.prettify(caps_string_neg) == caps_string_neg
# test camelCase
camel_case_string = "testing_one_two_three"
assert parse.prettify(camel_case_string, camelCase=True) == "Testing One Two Three"
# test remove comma
remove_comma_string = "remove,the,commas"
parse.prettify(remove_comma_string, removeComma=True)
assert parse.prettify(remove_comma_string, removeComma=True) == "removethecommas"
# test etal
etal_lower_string = "testing string Et Al Et al"
etal_strip_string = "nextstrain et al. et al Et Al."
assert parse.prettify(etal_lower_string, etal='lower') == etal_lower_string.lower()
assert parse.prettify(etal_strip_string, etal='strip') == "nextstrain "
def test_parse_sequence(self):
sequence_record = Bio.SeqRecord.SeqRecord(
seq=Bio.Seq.Seq("ATCG"),
id="sequence_A",
description="sequence_A|USA|2020-10-03|north_america"
)
fields = ["strain", "country", "date", "region"]
sequence, metadata = parse.parse_sequence(
sequence_record,
fields=fields,
strain_key="strain",
prettify_fields=["region"]
)
assert sequence.id == metadata["strain"]
assert sequence.id == "sequence_A"
assert set(fields) == set(metadata.keys())
assert metadata["region"] == "North America"
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