"""Tests of parsers for dealing with NCBI Taxonomy files. """ from unittest import TestCase from cogent3.parse.ncbi_taxonomy import ( MissingParentError, NcbiName, NcbiNameLookup, NcbiNameParser, NcbiTaxon, NcbiTaxonLookup, NcbiTaxonomyFromFiles, NcbiTaxonParser, ) good_nodes = """1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 2\t|\t1\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 6\t|\t2\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t|\t 7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 9\t|\t7\t|\tsubspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 10\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| """.split( "\n" ) bad_nodes = """1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 2\t|\t1\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 6\t|\t2\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t|\t 7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 9\t|\t777\t|\tsubspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 10\t|\t666\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| """.split( "\n" ) good_names = """1\t|\tall\t|\t\t|\tsynonym\t| 1\t|\troot\t|\t\t|\tscientific name\t| 2\t|\tBacteria\t|\tBacteria \t|\tscientific name\t| 2\t|\tMonera\t|\tMonera \t|\tin-part\t| 2\t|\tProcaryotae\t|\tProcaryotae <#1>\t|\tin-part\t| 2\t|\tProkaryotae\t|\tProkaryotae <#1>\t|\tin-part\t| 2\t|\teubacteria\t|\t\t|\tgenbank common name\t| 6\t|\tAzorhizobium\t|\t\t|\tscientific name\t| 7\t|\tAzorhizobium caulinodans\t|\t\t|\tscientific name\t| 9\t|\tBuchnera aphidicola\t|\t\t|\tscientific name\t| 10\t|\tFakus namus\t|\t\t|\tscientific name\t| """.split( "\n" ) class NcbiTaxonTests(TestCase): """Tests proper parsing of NCBI node file, e.g. nodes.dmp""" def test_init(self): """NcbiTaxon init should return object containing taxonomy data""" good_1 = """1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n""" good_2 = """2\t|\t1\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n""" good_3 = """6\t|\t2\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t|\n""" good_4 = """7\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n""" node_1 = NcbiTaxon(good_1) # make a NcbiTaxon object node_2 = NcbiTaxon(good_2) # from the corresponding node_3 = NcbiTaxon(good_3) # line. node_4 = NcbiTaxon(good_4) self.assertEqual(node_1.Rank, "no rank") # confirm object holds self.assertEqual(node_1.RankId, 28) # right data self.assertEqual(node_1.ParentId, 1) self.assertEqual(node_2.Rank, "superkingdom") self.assertEqual(node_2.RankId, 27) self.assertEqual(node_2.ParentId, 1) self.assertEqual(node_3.Rank, "genus") self.assertEqual(node_3.RankId, 8) self.assertEqual(node_3.ParentId, 2) self.assertEqual(node_4.Rank, "species") self.assertEqual(node_4.RankId, 4) self.assertEqual(node_4.ParentId, 6) # test some comparisons assert node_1 > node_2 assert node_1 > node_3 assert node_1 > node_4 assert node_1 == node_1 assert node_2 < node_1 assert node_2 == node_2 assert node_4 < node_1 assert node_3 > node_4 def test_str(self): """NcbiTaxon str should write data in input format from nodes.dmp""" good = """2\t|\t1\t|\tsuperkingdom\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|\n""" node = NcbiTaxon(good) self.assertEqual(str(node), good) root = """1\t|\t1\t|\tno rank\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|""" NcbiTaxon(root) self.assertEqual(str(root), root) def test_bad_input(self): """NcbiTaxon init should raise ValueError if nodes missing""" bad_node_taxid = """\t|\t6\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n""" # contains no taxon_id; not valid bad_node_parentid = """7\t|\t\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t|\n""" # contains no parent_id; not valid self.assertRaises(ValueError, NcbiTaxon, bad_node_taxid) self.assertRaises(ValueError, NcbiTaxon, bad_node_parentid) class NcbiNameTests(TestCase): """Tests proper parsing NCBI name file, e.g. names.dmp.""" def test_init(self): """NcbiName should init OK with well-formed name line""" line_1 = """1\t|\tall\t|\t\t|\tsynonym\t|\n""" line_2 = """1\t|\troot\t|\t\t|\tscientific name\t|\n""" line_3 = """2\t|\tBacteria\t|\tBacteria \t|\tscientific name\t|\n""" line_4 = """7\t|\tAzorhizobium caulinodans\t|\t\t|\tscientific name\t|\n""" name_1 = NcbiName(line_1) # make an NcbiName object name_2 = NcbiName(line_2) # from the corresponding line name_3 = NcbiName(line_3) name_4 = NcbiName(line_4) self.assertEqual(name_1.TaxonId, 1) # test that the data self.assertEqual(name_1.NameClass, "synonym") # fields in the object self.assertEqual(name_2.TaxonId, 1) # hold right data self.assertEqual(name_2.NameClass, "scientific name") self.assertEqual(name_3.TaxonId, 2) self.assertEqual(name_3.NameClass, "scientific name") self.assertEqual(name_4.TaxonId, 7) self.assertEqual(name_4.NameClass, "scientific name") def test_str(self): """NcbiName str should return line in original format""" line = """1\t|\troot\t|\t\t|\tscientific name|\n""" name = NcbiName(line) self.assertEqual(str(name), line) def test_bad_input(self): """NcbiName init should raise correct errors on bad data""" bad_name_taxid = """\t|\troot\t|\t\t|\tscientific name\t|\n""" # no tax_id self.assertRaises(ValueError, NcbiName, bad_name_taxid) class NcbiNameLookupTest(TestCase): """Tests of the NcbiNameLookup factory function.""" def test_init(self): """NcbiNameLookup should map taxon ids to scientific names""" names = list(NcbiNameParser(good_names)) # list of objects sci_names = NcbiNameLookup(names) # NcbiNameLookup object root = names[1] # NcbiName object made from 2nd line of good_name_file bacteria = names[2] # from 3rd line of good_name_file azorhizobium = names[7] caulinodans = names[8] assert sci_names[1] is root # gets NcbiName object from the assert sci_names[2] is bacteria # NcbiNameLookup object and assert sci_names[6] is azorhizobium # asks if it is the original assert sci_names[7] is caulinodans # NcbiName object self.assertEqual(sci_names[1].Name, "root") self.assertEqual(sci_names[2].Name, "Bacteria") self.assertEqual(sci_names[7].Name, "Azorhizobium caulinodans") self.assertEqual(sci_names[9].Name, "Buchnera aphidicola") class NcbiTaxonLookupTest(TestCase): """Tests of the NcbiTaxonLookup factory function.""" def setUp(self): """Sets up the class tests""" self.names = list(NcbiNameParser(good_names)) self.nodes = list(NcbiTaxonParser(good_nodes)) self.taxID_to_obj = NcbiTaxonLookup(self.nodes) self.names_to_obj = NcbiNameLookup(self.names) def test_init(self): """NcbiTaxonLookup should have correct fields for input NcbiTaxon""" line1_obj = self.nodes[0] # NcbiTaxon objects made from lines of line2_obj = self.nodes[1] # good_node_file line3_obj = self.nodes[2] line4_obj = self.nodes[3] line5_obj = self.nodes[4] # gets NcbiTaxon object from assert self.taxID_to_obj[1] is line1_obj assert self.taxID_to_obj[2] is line2_obj # NcbiTaxonLookup object & # asks if it is the original assert self.taxID_to_obj[6] is line3_obj assert self.taxID_to_obj[7] is line4_obj # NcbiTaxon object assert self.taxID_to_obj[9] is line5_obj self.assertEqual(self.taxID_to_obj[1].ParentId, 1) # checking a few self.assertEqual(self.taxID_to_obj[2].ParentId, 1) # individual self.assertEqual(self.taxID_to_obj[6].ParentId, 2) # fields of the self.assertEqual(self.taxID_to_obj[7].ParentId, 6) # NcbiTaxon objs self.assertEqual(self.taxID_to_obj[9].ParentId, 7) self.assertEqual(self.taxID_to_obj[1].Rank, "no rank") self.assertEqual(self.taxID_to_obj[2].Rank, "superkingdom") self.assertEqual(self.taxID_to_obj[6].Rank, "genus") self.assertEqual(self.taxID_to_obj[7].Rank, "species") self.assertEqual(self.taxID_to_obj[7].EmblCode, "AC") self.assertEqual(self.taxID_to_obj[7].DivisionId, "0") self.assertEqual(self.taxID_to_obj[7].DivisionInherited, 1) self.assertEqual(self.taxID_to_obj[7].TranslTable, 11) self.assertEqual(self.taxID_to_obj[7].TranslTableInherited, 1) self.assertEqual(self.taxID_to_obj[7].TranslTableMt, 0) self.assertEqual(self.taxID_to_obj[7].TranslTableMtInherited, 1) class NcbiTaxonomyTests(TestCase): """Tests of the NcbiTaxonomy class.""" def setUp(self): self.tx = NcbiTaxonomyFromFiles(good_nodes, good_names) def test_init_good(self): """NcbiTaxonomyFromFiles should pass spot-checks of resulting objects""" self.assertEqual(len(self.tx.ByName), 6) self.assertEqual(len(self.tx.ById), 6) self.assertEqual(self.tx[10].Name, "Fakus namus") self.assertEqual(self.tx["1"].Name, "root") self.assertEqual(self.tx["root"].parent, None) self.assertEqual(self.tx.Deadbeats, {}) def test_init_bad(self): """NcbiTaxonomyFromFiles should produce deadbeats by default""" bad_tx = NcbiTaxonomyFromFiles(bad_nodes, good_names) self.assertEqual(len(bad_tx.Deadbeats), 2) assert 777 in bad_tx.Deadbeats assert 666 in bad_tx.Deadbeats assert bad_tx.Deadbeats[777] == bad_tx[9] def test_init_strict(self): """NcbiTaxonomyFromFiles should fail if strict and deadbeats exist""" tx = NcbiTaxonomyFromFiles(good_nodes, good_names, strict=True) self.assertRaises( MissingParentError, NcbiTaxonomyFromFiles, bad_nodes, good_names, strict=True, ) def test_Ancestors(self): """NcbiTaxonomy should support Ancestors correctly, not incl. self""" result = self.tx["7"].ancestors() tax_ids = [taxon_obj.TaxonId for taxon_obj in result] self.assertEqual(tax_ids, [6, 2, 1]) def test_Parent(self): """NcbiTaxonomy should support parent correctly""" assert self.tx[7].parent is self.tx[6] assert self.tx[6].parent is self.tx[2] assert self.tx[2].parent is self.tx[1] assert self.tx[1].parent is None def test_Siblings(self): """NcbiTaxonomy should support Siblings correctly""" sibs = self.tx[7].siblings() self.assertEqual(len(sibs), 1) assert sibs[0] is self.tx[10] def test_Children(self): """NcbiTaxonomy should support children correctly""" children = self.tx[6].children self.assertEqual(len(children), 2) assert children[0] is self.tx[7] assert children[1] is self.tx[10] root_kids = self.tx["root"] self.assertEqual(len(root_kids), 1) assert root_kids[0] is self.tx[2] self.assertEqual(len(self.tx[10].children), 0) def test_Names(self): """NcbiTaxonomy should fill in names correctly""" self.assertEqual(self.tx["6"].Name, "Azorhizobium") self.assertEqual(self.tx["1"].Name, "root") self.assertEqual(self.tx["2"].Name, "Bacteria") self.assertEqual(self.tx["7"].Name, "Azorhizobium caulinodans") def test_last_common_ancestor(self): """NcbiTaxonomy should support last_common_ancestor()""" assert self.tx[9].last_common_ancestor(self.tx[9]) is self.tx[9] assert self.tx[9].last_common_ancestor(self.tx[7]) is self.tx[7] assert self.tx[9].last_common_ancestor(self.tx[10]) is self.tx[6] assert self.tx[9].last_common_ancestor(self.tx[1]) is self.tx[1] class NcbiTaxonNodeTests(TestCase): """Tests of the NcbiTaxonNode class. Note: only testing methods that differ from the TreeNode base class. Note: nested_species is explicitly designed to test the case where the nodes file does _not_ contain the root, and where the id of the de facto root is not 1, to make sure there's nothing special about a node called 'root' or with id 1. """ def test_getRankedDescendants(self): """NcbiTaxonNode getRankedDescendants should return correct list""" nested_species = """3\t|\t3\t|\tsuperkingdom\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 11\t|\t3\t|\tkingdom\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 22\t|\t11\t|\tclass\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 44\t|\t22\t|\torder\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 66\t|\t22\t|\torder\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t|\t 77\t|\t66\t|\tfamily\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 99\t|\t66\t|\tfamily\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 88\t|\t44\t|\tfamily\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 101\t|\t77\t|\tgenus\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 202\t|\t77\t|\tgenus\t|\t\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 606\t|\t99\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t|\t 707\t|\t88\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 909\t|\t88\t|\tgenus\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 123\t|\t909\t|\tgroup\t|\t\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 1111\t|\t123\t|\tspecies\t|\tAT\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 2222\t|\t707\t|\tspecies\t|\tTT\t|\t0\t|\t0\t|\t11\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t| 6666\t|\t606\t|\tspecies\t|\tGG\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t|\t 7777\t|\t606\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 9999\t|\t202\t|\tspecies\t|\tBA\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 1010\t|\t101\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 5555\t|\t555\t|\tspecies\t|\tAC\t|\t0\t|\t1\t|\t11\t|\t1\t|\t0\t|\t1\t|\t0\t|\t0\t|\t\t| 555\t|\t3\t|\tsuperclass\t|\t\t|\t8\t|\t0\t|\t1\t|\t0\t|\t0\t|\t0\t|\t0\t|\t0\t|\t\t|""".split( "\n" ) nested_names = [ "3|a||scientific name|", "11|b||scientific name|", "555|c||scientific name|", "22|d||scientific name|", "44|e||scientific name|", "66|f||scientific name|", "88|g||scientific name|", "77|h||scientific name|", "99|i||scientific name|", "707|j||scientific name|", "909|k||scientific name|", "101|l||scientific name|", "202|m||scientific name|", "606|n||scientific name|", "2222|o||scientific name|", "123|p||scientific name|", "1111|q||scientific name|", "1010|r||scientific name|", "9999|s||scientific name|", "7777|t||scientific name|", "6666|u||scientific name|", "5555|z||scientific name|", ] tx = NcbiTaxonomyFromFiles(nested_species, nested_names) dec = tx[3].getRankedDescendants("superclass") self.assertEqual(len(dec), 1) assert dec[0] is tx[555] sp = tx["f"].getRankedDescendants("species") self.assertCountEqual(sp, [tx[1010], tx[9999], tx[7777], tx[6666]]) empty = tx[11].getRankedDescendants("superclass") self.assertEqual(empty, []) gr = tx[3].getRankedDescendants("group") self.assertEqual(gr, [tx[123]]) assert tx[3] is tx["a"]