# ---------------------------------------------------------------------------- # Copyright (c) 2019-2023, QIIME 2 development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- import qiime2 from qiime2.plugin.testing import TestPluginBase from qiime2 import Metadata from q2_types.feature_data import TSVTaxonomyFormat import pandas as pd from rescript.edit_taxonomy import edit_taxonomy import_data = qiime2.Artifact.import_data class TestReplaceTaxonomy(TestPluginBase): package = 'rescript.tests' def setUp(self): super().setUp() # setup taxonomy to be edited tax_fp = self.get_data_path('escherichia_shigella_taxonomy.txt') self.taxonomy = TSVTaxonomyFormat(tax_fp, mode='r').view(pd.Series) # setup full string replacement replc = self.get_data_path('taxonomy-replacement-full-strings.txt') md_replc = Metadata.load(replc) self.md_replc_col = md_replc.get_column('replacements') # setup substring replacement ss_replc = self.get_data_path('taxonomy-replacement-pass.txt') md_ss_replc = Metadata.load(ss_replc) self.md_ss_replc_col = md_ss_replc.get_column('replacements') # setup substring regex replacement ssr_replc = self.get_data_path('taxonomy-replacement-regex.txt') md_ssr_replc = Metadata.load(ssr_replc) self.md_ssr_replc_col = md_ssr_replc.get_column('replacements') # setup reusable dicts self.exp_dict_00 = {'Sal01': ('d__SUPER_DUPER_BACTERIA; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'Sal02': ('d__SUPER_DUPER_BACTERIA; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'UncultSal': ('d__SUPER_DUPER_BACTERIA; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__uncultured_Salmonella'), 'Esch01': ('d__SUPER_DUPER_BACTERIA; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; s__'), 'Shig01': ('d__SUPER_DUPER_BACTERIA; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; s__')} self.exp_dict_01 = {'Sal01': ('d__Bacteria; p__LAME-PYHLA; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'Sal02': ('d__Bacteria; p__LAME-PYHLA; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'UncultSal': ('d__Bacteria; ' 'p__LAME-PYHLA; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__UNCIVILIZED_Salmonella'), 'Esch01': ('d__Bacteria; p__LAME-PYHLA; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; s__'), 'Shig01': ('d__Bacteria; p__LAME-PYHLA; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; s__')} self.exp_dict_02 = {'Sal01': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'Sal02': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'UncultSal': ('d__Bacteria; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__uncultured_Salmonella'), 'Esch01': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__unknown_Escherichia-Shigella'), 'Shig01': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__unknown_Escherichia-Shigella')} self.exp_dict_03 = {'Sal01': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'Sal02': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__Salmonella_enterica'), 'UncultSal': ('d__Bacteria; ' 'p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__UNCIVIL_Salmonella'), 'Esch01': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__unknown_Escherichia-Shigella'), 'Shig01': ('d__Bacteria; p__Proteobacteria; ' 'c__Gammaproteobacteria; ' 'o__Enterobacterales; ' 'f__Enterobacteriaceae; ' 'g__Escherichia-Shigella; ' 's__unknown_Escherichia-Shigella')} def test_edit_taxonomy_pass(self): obs_series = edit_taxonomy(taxonomy=self.taxonomy, replacement_map=self.md_ss_replc_col, use_regex=False) obs_dict = obs_series.to_dict() self.maxDiff = None self.assertEqual(obs_dict, self.exp_dict_00) def test_edit_taxonomy_pass_full_string(self): obs_series = edit_taxonomy(taxonomy=self.taxonomy, replacement_map=self.md_replc_col, use_regex=False) obs_dict = obs_series.to_dict() self.maxDiff = None self.assertEqual(obs_dict, self.exp_dict_02) def test_edit_taxonomy_pass_regex(self): obs_series = edit_taxonomy(taxonomy=self.taxonomy, replacement_map=self.md_ssr_replc_col, use_regex=True) obs_dict = obs_series.to_dict() self.maxDiff = None self.assertEqual(obs_dict, self.exp_dict_01) def test_edit_taxonomy_pass_regex_cl(self): ss = ['p__.*; c__', 's__uncultured', 'g__Escherichia.*; s__', r'g__\[Salmonella\]', 'g__Shigella'] rs = ['p__LAME-PYHLA; c__', 's__UNCIVILIZED', 'g__Escherichia-Shigella; s__', 'g__Escherichia-Shigella', 'g__Escherichia-Shigella'] obs_series = edit_taxonomy(taxonomy=self.taxonomy, search_strings=ss, replacement_strings=rs, use_regex=True) obs_dict = obs_series.to_dict() self.maxDiff = None self.assertEqual(obs_dict, self.exp_dict_01) def test_edit_taxonomy_pass_cl(self): ss = ['g__[Salmonella]', 'g__Escherichia;', 'g__Shigella', 'd__Bacteria;'] rs = ['g__Escherichia-Shigella', 'g__Escherichia-Shigella;', 'g__Escherichia-Shigella', 'd__SUPER_DUPER_BACTERIA;'] obs_series = edit_taxonomy(taxonomy=self.taxonomy, search_strings=ss, replacement_strings=rs, use_regex=False) obs_dict = obs_series.to_dict() self.maxDiff = None self.assertEqual(obs_dict, self.exp_dict_00) def test_edit_taxonomy_unequal_string_lists_fail_cl(self): ss = ['g__[Salmonella]', 'g__Escherichia;', 'g__Shigella'] rs = ['g__Escherichia-Shigella', 'g__Escherichia-Shigella;', 'g__Escherichia-Shigella', 'd__SUPER_DUPER_BACTERIA;'] self.assertRaises(ValueError, edit_taxonomy, taxonomy=self.taxonomy, search_strings=ss, replacement_strings=rs) def test_merge_cl_and_map_file(self): ss = ['s__uncultured_Salmonella'] rs = ['s__UNCIVIL_Salmonella'] obs_series = edit_taxonomy(taxonomy=self.taxonomy, replacement_map=self.md_replc_col, search_strings=ss, replacement_strings=rs, use_regex=False) obs_dict = obs_series.to_dict() self.maxDiff = None self.assertEqual(obs_dict, self.exp_dict_03) def test_unequal_ranks(self): with self.assertWarnsRegex(UserWarning, "Warning: the number of " "taxonomy ranks in the output "): ss = ['d__Bacter.*__'] rs = ['d__BAD_REPLACEMENT'] edit_taxonomy(taxonomy=self.taxonomy, search_strings=ss, replacement_strings=rs, use_regex=True)