def test_fast_versus_slow():
df = pd.DataFrame({"Sample": "001", "epitope": ["AAAAL"] * 1000, "iedb_epitope": ["AGGGT"] * 1000})
from timeit import Timer
slow_timer = Timer(lambda: calculate_similarity_from_df(df, ignore_seqalign=True))
slow_time = slow_timer.timeit(number=3)
fast_timer = Timer(lambda: calculate_similarity_from_df(df, ignore_seqalign=False))
fast_time = fast_timer.timeit(number=3)
ok_(
slow_time > fast_time * 5,
("The fast similarity calculation (%0.2f) should be at least " "5x faster than the slower version (%0.2f).")
% (fast_time, slow_time),
)
def test_fast_versus_slow():
df = pd.DataFrame({'Sample': '001',
'epitope': ['AAAAL'] * 1000,
'iedb_epitope': ['AGGGT'] * 1000})
from timeit import Timer
slow_timer = Timer(lambda: calculate_similarity_from_df(df, ignore_seqalign=True))
slow_time = slow_timer.timeit(number=3)
fast_timer = Timer(lambda: calculate_similarity_from_df(df, ignore_seqalign=False))
fast_time = fast_timer.timeit(number=3)
ok_(slow_time > fast_time * 5,
("The fast similarity calculation (%0.2f) should be at least "
"5x faster than the slower version (%0.2f).") % (
fast_time, slow_time))
def test_single_comparison_ignore_seqalign():
df = pd.DataFrame({'Sample': '001',
'epitope': ['AAALPGKCGV'],
'iedb_epitope': ['EFKEFAAGRR']})
df_scores = calculate_similarity_from_df(df, ignore_seqalign=True)
# TODO: This score is currently unverified
eq_(df_scores.score.max(), 2.38)
def test_single_comparison():
# TODO: Figure out why this doesn't work when trim_seq isn't used
# Error: https://github.com/ekg/vcflib/blob/master/src/ssw.c#L556
df = pd.DataFrame({'Sample': '001',
'epitope': ['AAALPGKCGV'],
'iedb_epitope': ['EFKEFAAGRR']})
df_scores = calculate_similarity_from_df(df)
# TODO: This score is currently unverified
eq_(df_scores.score.max(), 2.38)
def test_single_comparison_ignore_seqalign():
df = pd.DataFrame({
'Sample': '001',
'epitope': ['AAALPGKCGV'],
'iedb_epitope': ['EFKEFAAGRR']
})
df_scores = calculate_similarity_from_df(df, ignore_seqalign=True)
# TODO: This score is currently unverified
eq_(df_scores.score.max(), 2.38)
def test_single_comparison():
# TODO: Figure out why this doesn't work when trim_seq isn't used
# Error: https://github.com/ekg/vcflib/blob/master/src/ssw.c#L556
df = pd.DataFrame({
'Sample': '001',
'epitope': ['AAALPGKCGV'],
'iedb_epitope': ['EFKEFAAGRR']
})
df_scores = calculate_similarity_from_df(df)
# TODO: This score is currently unverified
eq_(df_scores.score.max(), 2.38)
