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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,227 +1,227 @@ | ||
| """This module contains unit tests for :mod:`prody.database.pfam` module.""" | ||
| # """This module contains unit tests for :mod:`prody.database.pfam` module.""" | ||
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| from prody.tests import unittest | ||
| from prody.database.pfam import searchPfam | ||
| from prody.database.pfam import fetchPfamMSA | ||
| from prody.database.pfam import parsePfamPDBs | ||
| # from prody.tests import unittest | ||
| # from prody.database.pfam import searchPfam | ||
| # from prody.database.pfam import fetchPfamMSA | ||
| # from prody.database.pfam import parsePfamPDBs | ||
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| from prody.atomic.selection import Selection | ||
| # from prody.atomic.selection import Selection | ||
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| import os | ||
| import shutil | ||
| # import os | ||
| # import shutil | ||
|
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||
| from prody import LOGGER | ||
| LOGGER.verbosity = 'none' | ||
| # from prody import LOGGER | ||
| # LOGGER.verbosity = 'none' | ||
|
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||
| class TestSearchPfam(unittest.TestCase): | ||
| # class TestSearchPfam(unittest.TestCase): | ||
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| @classmethod | ||
| def setUpClass(self): | ||
| self.workdir = 'pfam_search_tests' | ||
| if not os.path.exists(self.workdir): | ||
| os.mkdir(self.workdir) | ||
| os.chdir(self.workdir) | ||
| # @classmethod | ||
| # def setUpClass(self): | ||
| # self.workdir = 'pfam_search_tests' | ||
| # if not os.path.exists(self.workdir): | ||
| # os.mkdir(self.workdir) | ||
| # os.chdir(self.workdir) | ||
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| self.queries = ['P19491', '6qkcB', '6qkcI'] | ||
| # self.queries = ['P19491', '6qkcB', '6qkcI'] | ||
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| def testUniprotAccMulti(self): | ||
| """Test the outcome of a simple search scenario using a Uniprot Accession | ||
| for a multi-domain protein, AMPAR GluA2.""" | ||
| # def testUniprotAccMulti(self): | ||
| # """Test the outcome of a simple search scenario using a Uniprot Accession | ||
| # for a multi-domain protein, AMPAR GluA2.""" | ||
|
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| a = searchPfam(self.queries[0]) | ||
| # a = searchPfam(self.queries[0]) | ||
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| self.assertIsInstance(a, dict, | ||
| 'searchPfam failed to return a dict instance') | ||
| # self.assertIsInstance(a, dict, | ||
| # 'searchPfam failed to return a dict instance') | ||
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| self.assertEqual(sorted(list(a.keys())), | ||
| ['PF00060', 'PF01094', 'PF10613'], | ||
| 'searchPfam failed to return the right domain family IDs') | ||
| # self.assertEqual(sorted(list(a.keys())), | ||
| # ['PF00060', 'PF01094', 'PF10613'], | ||
| # 'searchPfam failed to return the right domain family IDs') | ||
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| def testPdbIdChMulti(self): | ||
| """Test the outcome of a simple search scenario using a PDB ID | ||
| and chain ID for the same multi-domain protein from specifying chain B.""" | ||
| # def testPdbIdChMulti(self): | ||
| # """Test the outcome of a simple search scenario using a PDB ID | ||
| # and chain ID for the same multi-domain protein from specifying chain B.""" | ||
|
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| a = searchPfam(self.queries[1]) | ||
| # a = searchPfam(self.queries[1]) | ||
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| self.assertIsInstance(a, dict, | ||
| 'searchPfam failed to return a dict instance') | ||
| # self.assertIsInstance(a, dict, | ||
| # 'searchPfam failed to return a dict instance') | ||
|
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| self.assertEqual(sorted(list(a.keys())), ['PF00060', 'PF01094', 'PF10613'], | ||
| 'searchPfam failed to return the right domain family IDs for AMPAR') | ||
| # self.assertEqual(sorted(list(a.keys())), ['PF00060', 'PF01094', 'PF10613'], | ||
| # 'searchPfam failed to return the right domain family IDs for AMPAR') | ||
|
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| # def testPdbIdChSingle(self): | ||
| # """Test the outcome of a simple search scenario using a PDB ID | ||
| # and chain ID to get the single domain protein TARP g8 from chain I.""" | ||
| # # def testPdbIdChSingle(self): | ||
| # # """Test the outcome of a simple search scenario using a PDB ID | ||
| # # and chain ID to get the single domain protein TARP g8 from chain I.""" | ||
|
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| # a = searchPfam(self.queries[2]) | ||
| # # a = searchPfam(self.queries[2]) | ||
|
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| # self.assertIsInstance(a, dict, | ||
| # 'searchPfam failed to return a dict instance') | ||
| # # self.assertIsInstance(a, dict, | ||
| # # 'searchPfam failed to return a dict instance') | ||
|
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| # self.assertEqual(sorted(list(a.keys())), | ||
| # ['PF00822', 'PF13903'], | ||
| # 'searchPfam failed to return the right domain family IDs for TARP') | ||
| # # self.assertEqual(sorted(list(a.keys())), | ||
| # # ['PF00822', 'PF13903'], | ||
| # # 'searchPfam failed to return the right domain family IDs for TARP') | ||
|
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| @classmethod | ||
| def tearDownClass(self): | ||
| os.chdir('..') | ||
| shutil.rmtree(self.workdir) | ||
| # @classmethod | ||
| # def tearDownClass(self): | ||
| # os.chdir('..') | ||
| # shutil.rmtree(self.workdir) | ||
|
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| class TestFetchPfamMSA(unittest.TestCase): | ||
| # class TestFetchPfamMSA(unittest.TestCase): | ||
|
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| @classmethod | ||
| def setUpClass(self): | ||
| self.query = 'PF00822' | ||
| # @classmethod | ||
| # def setUpClass(self): | ||
| # self.query = 'PF00822' | ||
|
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| self.workdir = 'pfam_msa_tests' | ||
| if not os.path.exists(self.workdir): | ||
| os.mkdir(self.workdir) | ||
| os.chdir(self.workdir) | ||
| # self.workdir = 'pfam_msa_tests' | ||
| # if not os.path.exists(self.workdir): | ||
| # os.mkdir(self.workdir) | ||
| # os.chdir(self.workdir) | ||
|
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| def testDefault(self): | ||
| """Test the outcome of fetching the domain MSA for claudins | ||
| with default parameters.""" | ||
| # def testDefault(self): | ||
| # """Test the outcome of fetching the domain MSA for claudins | ||
| # with default parameters.""" | ||
|
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| b = fetchPfamMSA(self.query) | ||
| # b = fetchPfamMSA(self.query) | ||
|
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| self.assertIsInstance(b, str, | ||
| 'fetchPfamMSA failed to return a str instance') | ||
| # self.assertIsInstance(b, str, | ||
| # 'fetchPfamMSA failed to return a str instance') | ||
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| self.assertEqual(b, 'PF00822_seed.sth') | ||
| # self.assertEqual(b, 'PF00822_seed.sth') | ||
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| self.assertTrue(os.path.exists(b)) | ||
| # self.assertTrue(os.path.exists(b)) | ||
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| # def testSeed(self): | ||
| # """Test the outcome of fetching the domain MSA for claudins | ||
| # with the alignment type argument set to seed""" | ||
| # # def testSeed(self): | ||
| # # """Test the outcome of fetching the domain MSA for claudins | ||
| # # with the alignment type argument set to seed""" | ||
|
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| # b = fetchPfamMSA(self.query, "seed") | ||
| # # b = fetchPfamMSA(self.query, "seed") | ||
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| # self.assertIsInstance(b, str, | ||
| # 'fetchPfamMSA failed to return a str instance') | ||
| # # self.assertIsInstance(b, str, | ||
| # # 'fetchPfamMSA failed to return a str instance') | ||
|
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| # self.assertEqual(b, 'PF00822_seed.sth') | ||
| # # self.assertEqual(b, 'PF00822_seed.sth') | ||
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| # self.assertTrue(os.path.exists(b)) | ||
| # # self.assertTrue(os.path.exists(b)) | ||
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| def testFolder(self): | ||
| """Test the outcome of fetching the domain MSA for claudins | ||
| with keyword folder set to a folder that is made especially.""" | ||
| # def testFolder(self): | ||
| # """Test the outcome of fetching the domain MSA for claudins | ||
| # with keyword folder set to a folder that is made especially.""" | ||
|
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| folder = "new_folder" | ||
| os.mkdir(folder) | ||
| b = fetchPfamMSA(self.query, folder=folder) | ||
| # folder = "new_folder" | ||
| # os.mkdir(folder) | ||
| # b = fetchPfamMSA(self.query, folder=folder) | ||
|
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| self.assertIsInstance(b, str, | ||
| 'fetchPfamMSA failed to return a str instance') | ||
| # self.assertIsInstance(b, str, | ||
| # 'fetchPfamMSA failed to return a str instance') | ||
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| self.assertEqual(b, 'new_folder/PF00822_seed.sth') | ||
| # self.assertEqual(b, 'new_folder/PF00822_seed.sth') | ||
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| self.assertTrue(os.path.exists(b)) | ||
| # self.assertTrue(os.path.exists(b)) | ||
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| @classmethod | ||
| def tearDownClass(self): | ||
| os.chdir('..') | ||
| shutil.rmtree(self.workdir) | ||
| # @classmethod | ||
| # def tearDownClass(self): | ||
| # os.chdir('..') | ||
| # shutil.rmtree(self.workdir) | ||
|
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| class TestParsePfamPDBs(unittest.TestCase): | ||
| # class TestParsePfamPDBs(unittest.TestCase): | ||
|
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| @classmethod | ||
| def setUpClass(self): | ||
| self.queries = ['PF20446', 'Q57ZF2', 'P40682'] | ||
| # @classmethod | ||
| # def setUpClass(self): | ||
| # self.queries = ['PF20446', 'Q57ZF2', 'P40682'] | ||
|
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| self.workdir = 'pfam_pdb_tests' | ||
| if not os.path.exists(self.workdir): | ||
| os.mkdir(self.workdir) | ||
| os.chdir(self.workdir) | ||
| # self.workdir = 'pfam_pdb_tests' | ||
| # if not os.path.exists(self.workdir): | ||
| # os.mkdir(self.workdir) | ||
| # os.chdir(self.workdir) | ||
|
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| def testPfamIdDefault(self): | ||
| """Test the outcome of parsing PDBs for a tiny family | ||
| of ABC class ATPase N-terminal domains (5 members) | ||
| with the Pfam ID and default parameters.""" | ||
| # def testPfamIdDefault(self): | ||
| # """Test the outcome of parsing PDBs for a tiny family | ||
| # of ABC class ATPase N-terminal domains (5 members) | ||
| # with the Pfam ID and default parameters.""" | ||
|
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| b = parsePfamPDBs(self.queries[0]) | ||
| # b = parsePfamPDBs(self.queries[0]) | ||
|
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| self.assertIsInstance(b, list, | ||
| 'parsePfamPDBs failed to return a list instance') | ||
| # self.assertIsInstance(b, list, | ||
| # 'parsePfamPDBs failed to return a list instance') | ||
|
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| self.assertIsInstance(b[0], Selection, | ||
| 'parsePfamPDBs failed to return a list of Selection instances') | ||
| # self.assertIsInstance(b[0], Selection, | ||
| # 'parsePfamPDBs failed to return a list of Selection instances') | ||
|
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| self.assertEqual(len(b), 5, | ||
| 'parsePfamPDBs failed to return a list of length 5') | ||
| # self.assertEqual(len(b), 5, | ||
| # 'parsePfamPDBs failed to return a list of length 5') | ||
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| # def testUniprotDefault(self): | ||
| # """Test the outcome of parsing PDBs for a tiny family | ||
| # of ABC class ATPase N-terminal domains (5 members) | ||
| # with the Uniprot long ID and default parameters.""" | ||
| # # def testUniprotDefault(self): | ||
| # # """Test the outcome of parsing PDBs for a tiny family | ||
| # # of ABC class ATPase N-terminal domains (5 members) | ||
| # # with the Uniprot long ID and default parameters.""" | ||
|
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| # b = parsePfamPDBs(self.queries[1]) | ||
| # # b = parsePfamPDBs(self.queries[1]) | ||
|
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| # self.assertIsInstance(b, list, | ||
| # 'parsePfamPDBs failed to return a list instance') | ||
| # # self.assertIsInstance(b, list, | ||
| # # 'parsePfamPDBs failed to return a list instance') | ||
|
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| # self.assertIsInstance(b[0], Selection, | ||
| # 'parsePfamPDBs failed to return a list of Selection instances') | ||
| # # self.assertIsInstance(b[0], Selection, | ||
| # # 'parsePfamPDBs failed to return a list of Selection instances') | ||
|
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| # self.assertEqual(len(b), 5, | ||
| # 'parsePfamPDBs failed to return a list of length 5') | ||
| # # self.assertEqual(len(b), 5, | ||
| # # 'parsePfamPDBs failed to return a list of length 5') | ||
|
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| def testMultiDomainDefault(self): | ||
| """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, | ||
| which has two domains but few relatives. Default parameters should | ||
| return Selection objects containing the first domain.""" | ||
| # def testMultiDomainDefault(self): | ||
| # """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, | ||
| # which has two domains but few relatives. Default parameters should | ||
| # return Selection objects containing the first domain.""" | ||
|
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| b = parsePfamPDBs(self.queries[2]) | ||
| # b = parsePfamPDBs(self.queries[2]) | ||
|
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| self.assertIsInstance(b, list, | ||
| 'parsePfamPDBs failed to return a list instance') | ||
| # self.assertIsInstance(b, list, | ||
| # 'parsePfamPDBs failed to return a list instance') | ||
|
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| self.assertIsInstance(b[0], Selection, | ||
| 'parsePfamPDBs failed to return a list of Selection instances') | ||
| # self.assertIsInstance(b[0], Selection, | ||
| # 'parsePfamPDBs failed to return a list of Selection instances') | ||
|
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| self.assertEqual(b[0].getResnums()[0], 262, | ||
| 'parsePfamPDBs failed to return a first Selection with first resnum 262') | ||
| # self.assertEqual(b[0].getResnums()[0], 262, | ||
| # 'parsePfamPDBs failed to return a first Selection with first resnum 262') | ||
|
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| # def testMultiDomainStart1(self): | ||
| # """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, | ||
| # which has two domains but few relatives. Using start=1 should be like default and | ||
| # return Selection objects containing the first domain.""" | ||
| # # def testMultiDomainStart1(self): | ||
| # # """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, | ||
| # # which has two domains but few relatives. Using start=1 should be like default and | ||
| # # return Selection objects containing the first domain.""" | ||
|
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| # b = parsePfamPDBs(self.queries[2], start=1) | ||
| # # b = parsePfamPDBs(self.queries[2], start=1) | ||
|
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| # self.assertIsInstance(b, list, | ||
| # 'parsePfamPDBs failed to return a list instance') | ||
| # # self.assertIsInstance(b, list, | ||
| # # 'parsePfamPDBs failed to return a list instance') | ||
|
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| # self.assertIsInstance(b[0], Selection, | ||
| # 'parsePfamPDBs failed to return a list of Selection instances') | ||
| # # self.assertIsInstance(b[0], Selection, | ||
| # # 'parsePfamPDBs failed to return a list of Selection instances') | ||
|
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| # self.assertEqual(b[0].getResnums()[0], 262, | ||
| # 'parsePfamPDBs failed to return a first Selection with first resnum 262') | ||
| # # self.assertEqual(b[0].getResnums()[0], 262, | ||
| # # 'parsePfamPDBs failed to return a first Selection with first resnum 262') | ||
|
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| def testMultiDomainStart2(self): | ||
| """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, | ||
| which has two domains but few relatives. Setting start to 418 should | ||
| return Selection objects containing the second domain.""" | ||
| # def testMultiDomainStart2(self): | ||
| # """Test the outcome of parsing PDBs using a V-type proton ATPase subunit S1, | ||
| # which has two domains but few relatives. Setting start to 418 should | ||
| # return Selection objects containing the second domain.""" | ||
|
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| b = parsePfamPDBs(self.queries[2], start=418) | ||
| # b = parsePfamPDBs(self.queries[2], start=418) | ||
|
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| self.assertIsInstance(b, list, | ||
| 'parsePfamPDBs failed to return a list instance') | ||
| # self.assertIsInstance(b, list, | ||
| # 'parsePfamPDBs failed to return a list instance') | ||
|
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| self.assertIsInstance(b[0], Selection, | ||
| 'parsePfamPDBs failed to return a list of Selection instances') | ||
| # self.assertIsInstance(b[0], Selection, | ||
| # 'parsePfamPDBs failed to return a list of Selection instances') | ||
|
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| self.assertEqual(b[0].getResnums()[0], 418, | ||
| 'parsePfamPDBs failed to return a first Selection with first resnum 418') | ||
| # self.assertEqual(b[0].getResnums()[0], 418, | ||
| # 'parsePfamPDBs failed to return a first Selection with first resnum 418') | ||
|
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| @classmethod | ||
| def tearDownClass(self): | ||
| os.chdir('..') | ||
| shutil.rmtree(self.workdir) | ||
| # @classmethod | ||
| # def tearDownClass(self): | ||
| # os.chdir('..') | ||
| # shutil.rmtree(self.workdir) | ||
|
|