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TST: Fix python taxonomy tests due to biocore#473 change
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@fedarko
fedarko committed Feb 6, 2021
1 parent 0cec1de commit 096a0cc
Showing 1 changed file with 38 additions and 38 deletions.
76 changes: 38 additions & 38 deletions tests/python/test_taxonomy_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,51 +62,51 @@ def check_basic_case_worked(self, split_fm):
split_fm.loc["f1"],
pd.Series({
"Level 1": "k__Bacteria",
"Level 2": "p__Bacteroidetes",
"Level 3": "c__Bacteroidia",
"Level 4": "o__Bacteroidales",
"Level 5": "f__Bacteroidaceae",
"Level 6": "g__Bacteroides",
"Level 7": "s__",
"Level 2": "k__Bacteria; p__Bacteroidetes",
"Level 3": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia",
"Level 4": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales",
"Level 5": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae",
"Level 6": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides",
"Level 7": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__",
"Confidence": 0.95
}, name="f1")
)
assert_series_equal(
split_fm.loc["f2"],
pd.Series({
"Level 1": "k__Bacteria",
"Level 2": "p__Proteobacteria",
"Level 3": "c__Gammaproteobacteria",
"Level 4": "o__Pasteurellales",
"Level 5": "f__Pasteurellaceae",
"Level 6": "g__",
"Level 7": "s__",
"Level 2": "k__Bacteria; p__Proteobacteria",
"Level 3": "k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria",
"Level 4": "k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales",
"Level 5": "k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae",
"Level 6": "k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__",
"Level 7": "k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__; s__",
"Confidence": 0.8
}, name="f2")
)
assert_series_equal(
split_fm.loc["f3"],
pd.Series({
"Level 1": "k__Bacteria",
"Level 2": "p__Bacteroidetes",
"Level 3": "c__Bacteroidia",
"Level 4": "o__Bacteroidales",
"Level 5": "f__Bacteroidaceae",
"Level 6": "g__Bacteroides",
"Level 7": "s__uniformis",
"Level 2": "k__Bacteria; p__Bacteroidetes",
"Level 3": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia",
"Level 4": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales",
"Level 5": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae",
"Level 6": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides",
"Level 7": "k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__uniformis",
"Confidence": 0
}, name="f3")
)
assert_series_equal(
split_fm.loc["f4"],
pd.Series({
"Level 1": "k__Bacteria",
"Level 2": "p__Firmicutes",
"Level 3": "c__Bacilli",
"Level 4": "Unspecified",
"Level 5": "Unspecified",
"Level 6": "Unspecified",
"Level 7": "Unspecified",
"Level 2": "k__Bacteria; p__Firmicutes",
"Level 3": "k__Bacteria; p__Firmicutes; c__Bacilli",
"Level 4": "k__Bacteria; p__Firmicutes; c__Bacilli; Unspecified",
"Level 5": "k__Bacteria; p__Firmicutes; c__Bacilli; Unspecified; Unspecified",
"Level 6": "k__Bacteria; p__Firmicutes; c__Bacilli; Unspecified; Unspecified; Unspecified",
"Level 7": "k__Bacteria; p__Firmicutes; c__Bacilli; Unspecified; Unspecified; Unspecified; Unspecified",
"Confidence": 1
}, name="f4")
)
Expand Down Expand Up @@ -181,35 +181,35 @@ def test_split_taxonomy_rows_with_no_semicolons(self):
split_fm.loc["f1"],
pd.Series({
"Level 1": "birds aren't real",
"Level 2": "Unspecified",
"Level 3": "Unspecified",
"Level 2": "birds aren't real; Unspecified",
"Level 3": "birds aren't real; Unspecified; Unspecified",
"Confidence": 0.95
}, name="f1")
)
assert_series_equal(
split_fm.loc["f2"],
pd.Series({
"Level 1": "theyve been drones",
"Level 2": "Unspecified",
"Level 3": "Unspecified",
"Level 2": "theyve been drones; Unspecified",
"Level 3": "theyve been drones; Unspecified; Unspecified",
"Confidence": 0.8
}, name="f2")
)
assert_series_equal(
split_fm.loc["f3"],
pd.Series({
"Level 1": "all along :O",
"Level 2": "Unspecified",
"Level 3": "Unspecified",
"Level 2": "all along :O; Unspecified",
"Level 3": "all along :O; Unspecified; Unspecified",
"Confidence": 0
}, name="f3")
)
assert_series_equal(
split_fm.loc["f4"],
pd.Series({
"Level 1": "k__Bacteria",
"Level 2": "p__Firmicutes",
"Level 3": "c__Bacilli",
"Level 2": "k__Bacteria; p__Firmicutes",
"Level 3": "k__Bacteria; p__Firmicutes; c__Bacilli",
"Confidence": 1
}, name="f4")
)
Expand Down Expand Up @@ -293,12 +293,12 @@ def test_split_taxonomy_SILVA_annotation(self):
split_fm.loc["f0"],
pd.Series({
"Level 1": "D_0__Bacteria",
"Level 2": "D_1__Gemmatimonadetes",
"Level 3": "D_2__Gemmatimonadetes",
"Level 4": "D_3__Gemmatimonadales",
"Level 5": "D_4__Gemmatimonadaceae",
"Level 6": "D_5__Gemmatimonas",
"Level 7": "D_6__uncultured bacterium",
"Level 2": "D_0__Bacteria; D_1__Gemmatimonadetes",
"Level 3": "D_0__Bacteria; D_1__Gemmatimonadetes; D_2__Gemmatimonadetes",
"Level 4": "D_0__Bacteria; D_1__Gemmatimonadetes; D_2__Gemmatimonadetes; D_3__Gemmatimonadales",
"Level 5": "D_0__Bacteria; D_1__Gemmatimonadetes; D_2__Gemmatimonadetes; D_3__Gemmatimonadales; D_4__Gemmatimonadaceae",
"Level 6": "D_0__Bacteria; D_1__Gemmatimonadetes; D_2__Gemmatimonadetes; D_3__Gemmatimonadales; D_4__Gemmatimonadaceae; D_5__Gemmatimonas",
"Level 7": "D_0__Bacteria; D_1__Gemmatimonadetes; D_2__Gemmatimonadetes; D_3__Gemmatimonadales; D_4__Gemmatimonadaceae; D_5__Gemmatimonas; D_6__uncultured bacterium",
}, name="f0")
)

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