From 096a0cc3a4dc3a290833756d7711178b2362ed3e Mon Sep 17 00:00:00 2001 From: Marcus Fedarko Date: Fri, 5 Feb 2021 23:09:56 -0800 Subject: [PATCH] TST: Fix python taxonomy tests due to #473 change --- tests/python/test_taxonomy_utils.py | 76 ++++++++++++++--------------- 1 file changed, 38 insertions(+), 38 deletions(-) diff --git a/tests/python/test_taxonomy_utils.py b/tests/python/test_taxonomy_utils.py index 703a2d7c1..f47c9695f 100644 --- a/tests/python/test_taxonomy_utils.py +++ b/tests/python/test_taxonomy_utils.py @@ -62,12 +62,12 @@ 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") ) @@ -75,12 +75,12 @@ def check_basic_case_worked(self, split_fm): 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") ) @@ -88,12 +88,12 @@ def check_basic_case_worked(self, split_fm): 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") ) @@ -101,12 +101,12 @@ def check_basic_case_worked(self, split_fm): 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") ) @@ -181,8 +181,8 @@ 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") ) @@ -190,8 +190,8 @@ def test_split_taxonomy_rows_with_no_semicolons(self): 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") ) @@ -199,8 +199,8 @@ def test_split_taxonomy_rows_with_no_semicolons(self): 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") ) @@ -208,8 +208,8 @@ def test_split_taxonomy_rows_with_no_semicolons(self): 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") ) @@ -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") )