# Copyright 2011 by Wibowo Arindrarto (w.arindrarto@gmail.com) # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. import unittest from os.path import join, basename from Bio import SeqIO from Bio._py3k import _as_bytes test_data = { 'data_empty': { 'path': ['Abi', 'empty.ab1'], 'seq': 'NNNNN', 'qual': [0, 0, 0, 0, 0], 'sample': '226041_C-ME-19_pCAGseqF', 'sample_well': 'C10', 'machine_model': '3730', 'run_start': '2009-12-12 09:56:53', 'run_finish': '2009-12-12 11:44:49', }, 'data_3730': { 'path': ['Abi', '3730.ab1'], 'seq': 'GGGCGAGCKYYAYATTTTGGCAAGAATTGAGCTCTATGGCCACAACCATGGTGAGCAAGGGCGAGGAGGATAACATGGCCATCATCAAGGAGTTCATGCGCTTCAAGGTGCACATGGAGGGCTCCGTGAACGGCCACGAGTTCGAGATCGAGGGCGAGGGCGAGGGCCGCCCCTACGAGGGCACCCAGACCGCCAAGCTGAAGGTGACCAAGGGTGGCCCCCTGCCCTTCGCCTGGGACATCCTGTCCCCTCAGTTCATGTACGGCTCCAAGGCCTACGTGAAGCACCCCGCCGACATCCCCGACTACTTGAAGCTGTCCTTCCCCGAGGGCTTCAAGTGGGAGCGCGTGATGAACTTCGAGGACGGCGGCGTGGTGACCGTGACCCAGGACTCCTCCCTGCAGGACGGCGAGTTCATCTACAAGGTGAAGCTGCGCGGCACCAACTTCCCCTCCGACGGCCCCGTAATGCAGAAGAAGACCATGGGCTGGGAGGCCTCCTCCGAGCGGATGTACCCCGAGGACGGCGCCCTGAAGGGCGAGATCAAGCAGAGGCTGAAGCTGAAGGACGGCGGCCACTACGACGCTGAGGTCAAGACCACCTACAAGGCCAAGAAGCCCGTGCAGCTGCCCGGCGCCTACAACGTCAACATCAAGTTGGACATCACCTCCCACAACGAGGACTACACCATCGTGGAACAGTACGAACGCGCCGAGGGCCGCCACTCCACCGGCGGCATGGACGAGCTGTACAAGGGCGGCAGCGGCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAARACCCGCGCCGAGGTGAARTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAAGGGGCAYCGCACCTTTC', 'qual': [20, 3, 4, 4, 4, 6, 4, 4, 0, 0, 0, 6, 0, 10, 20, 26, 22, 17, 21, 31, 29, 32, 28, 18, 23, 17, 19, 35, 36, 50, 39, 50, 50, 50, 50, 50, 25, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 39, 33, 20, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 50, 35, 31, 23, 28, 31, 21, 43, 39, 35, 24, 30, 26, 35, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 31, 24, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 43, 43, 50, 50, 50, 50, 50, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 35, 50, 50, 50, 50, 31, 36, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 36, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 40, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 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55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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22, 39, 35, 35, 35, 35, 35, 35, 37, 38, 28, 35, 21, 36, 36, 37, 35, 35, 20, 39, 39, 35, 35, 35, 35, 37, 38, 28, 35, 37, 34, 35, 24, 24, 27, 25, 20, 24, 37, 35, 27, 21, 20, 21, 27, 17, 20, 24, 32, 26, 20, 12, 20, 10, 20, 24, 25, 23, 20, 32, 24, 24, 23, 20, 24, 23, 18, 34, 34, 34, 22, 26, 24, 24, 18, 22, 22, 23, 25, 20, 12, 20, 24, 23, 24, 23, 22, 20, 20, 0, 20, 24, 23, 20, 8, 10, 4, 20, 20, 3, 7, 19, 20, 4, 4, 7, 7, 0, 7, 11, 18, 8, 3, 23, 23, 20, 11, 4, 20, 18, 12, 20, 20, 20, 4, 20, 4, 2, 3, 21, 21, 21, 21, 10, 15, 14, 15, 19, 2, 4, 3, 6, 11, 3, 4, 6, 21, 16, 20, 11, 1, 4, 12, 0, 15, 8, 1, 3, 3, 12, 1, 11, 20, 4], 'sample': '226032_C-ME-18_pCAGseqF', 'sample_well': 'B9', 'dye': 'Z-BigDyeV3', 'polymer': 'POP7 ', 'machine_model': '3730', 'run_start': '2009-12-12 09:56:53', 'run_finish': '2009-12-12 11:44:49', }, 'data_3100': { 'path': ['Abi', '3100.ab1'], 'seq': 'CAAGATTGCATTCATGATCTACGATTACTAGCGATTCCAGCTTCATATAGTCGAGTTGCAGACTACAATCCGAACTGAGAACAACTTTATGGGATTTGCTTGACCTCGCGGTTTCGCTGCCCTTTGTATTGTCCATTGTAGCACGTGTGTAGCCCAAATCATAAGGGGCATGATGATTTGACGTCATCCCCACCTTCCTCCGGTTTGTCACCGGCAGTCAACTTAGAGTGCCCAACTTAATGATGGCAACTAAGCTTAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAACCATGCACCACCTGTCACTCTGTCCCCCGAAGGGGAAAACTCTATCTCTAGAGGAGTCAGAGGATGTCAAGATTTGGTAAGGTTCTTCGCGTTGCTTCGAATTAAACCACATGCTCCACCGCTTGTGCGGGTCCCCGTCAATTCCTTTGAGTTTCAACCTTGCGGTCGTACTCCCCAGGCGGAGTGCTTAATGCGTTAGCTGCAGCACTAAGGGGCGGAAACCCCCTAACACTTAGCACTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGATCCCCACGCTTTCGCACATCAGCGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTGCGCATTTCACCGCTACACATGGAAATTCCACTTTCCTCTTCTGCACTCAAGTTTTCCAGATTTCGATGAACCTTCAACGATGGAGGCCCGTGGCTTTTCACCATTCAAGGAACCTTTTA', 'qual': [5, 3, 4, 4, 4, 5, 9, 4, 4, 4, 5, 4, 4, 4, 4, 4, 6, 13, 23, 20, 15, 17, 10, 9, 13, 23, 18, 14, 19, 34, 15, 24, 34, 18, 30, 35, 41, 34, 22, 39, 53, 58, 35, 46, 24, 42, 46, 46, 54, 42, 53, 58, 52, 41, 22, 62, 52, 62, 52, 62, 41, 38, 16, 42, 62, 56, 62, 62, 62, 62, 62, 62, 54, 56, 39, 62, 49, 35, 19, 44, 44, 42, 62, 62, 62, 62, 54, 62, 62, 62, 62, 49, 49, 43, 39, 62, 62, 62, 62, 62, 62, 62, 59, 43, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 49, 59, 62, 62, 59, 59, 62, 62, 62, 62, 62, 59, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 59, 62, 62, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 59, 59, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 50, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 54, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 59, 59, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 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53, 47, 54, 54, 53, 54, 54, 54, 52, 54, 42, 47, 35, 42, 54, 45, 54, 53, 54, 23, 34, 24, 51, 52, 33, 46, 44, 33, 49, 51, 45, 53, 32, 52, 53, 52, 51, 36, 52, 53, 52, 52, 37, 53, 52, 40, 27, 24, 46, 16, 33, 45, 51, 43, 51, 51, 46, 46, 45, 42, 31, 43, 41, 43, 35, 43, 43, 42, 31, 46, 46, 32, 46, 35, 42, 46, 42, 31, 31, 43, 42, 35, 21, 42, 35, 28, 46, 47, 37, 41, 29, 39, 31, 32, 39, 31, 41, 43, 34, 43, 36, 27, 31, 27, 35, 36, 24, 44, 33, 31, 32, 38, 35, 31, 32, 29, 31, 31, 31, 38, 38, 36, 31, 34, 30, 21, 28, 32, 32, 47, 31, 33, 30, 23, 22, 25, 25, 26, 30, 30, 21, 28, 31, 21, 14, 5, 3, 16, 9, 18, 27, 8, 19, 4, 5, 13, 47, 27, 14, 21, 9, 17, 21, 17, 27, 14, 23, 23, 14, 15, 28, 15, 12, 8, 5, 3, 17, 28, 16, 13, 17, 11, 2, 2, 3, 29, 7, 3, 1, 3, 3, 8, 7, 7, 24, 12, 3, 4, 15, 3, 4, 7, 5, 1, 2, 2, 8, 24, 6, 4, 11, 23, 9, 6, 4, 3, 5, 3, 5, 17, 17, 22, 11, 4, 5, 8, 16, 10, 6, 11, 6, 11, 5, 5, 27, 18, 7, 15, 16, 30, 21, 14, 7], 'sample': '16S_S2_1387R', 'sample_well': 'H3', 'dye': 'Z-BigDyeV3', 'polymer': 'POP7 ', 'machine_model': '3100', 'run_start': '2010-01-27 09:52:45', 'run_finish': '2010-01-27 10:41:07', }, 'data_310': { 'path': ['Abi', '310.ab1'], 'seq': 'TGATNTTNACNNTTTTGAANCANTGAGTTAATAGCAATNCTTTACNAATAAGAATATACACTTTCTGCTTAGGGATGATAATTGGCAGGCAAGTGAATCCCTGAGCGTGNATTTGATAATGACCTAAATAATGGATGGGGTTTTAATTCCCAGACCTTCCCCTTTTTAANNGGNGGATTANTGGGGGNNNAACNNGGGGGGCCCTTNCCNAAGGGGGAAAAAATTTNAAACCCCCCNAGGNNGGGNAAAAAAAAATTTCCAAATTNCCGGGGTNNCCCCCAANTTTTTNCCGCNGGGAAAANNNNCCCCCCCNGGGNCCCCCCCCNNAAAAAAAAAAAAAAAAACCCCCCCCCCNTTGGGGNGGTNTNCNCCCCCNNANAANNGGGGGNNAAAAAAAAAGGCCCCCCCCAAAAAAAACCCNCNTTCTNNCNNNNNGNNCNGNNCCCCCNNCCNTNTNGGGGGGGGGGGNGGAAAAAAAACCCCTTTNTGNNNANANNAACCCNCTCNTNTTTTTTTTTTTANGNNNNCNNNNCAAAAAAAAANCNCCCCCNNCNNNCNNNCNCCCCNNNNTNAAAANANNAANNNNTTTTTTTNGGGGGGGTGNGCGNCCCNNANCNNNNNNNNGCGNGGNCNCCNNCCCNCNANAAANNNTNTTTTTTTTTTTTTTTNTNNTCNNCCCNNNCCCCNNCCCCCCCCCCCCCNCCNCNNNNNGGGGNNNCGGNNCNNNNNNNCCNTNCTNNANATNCCNTTNNNNNNNNGNNNNNNNNACNNNNNTNNTNNNCNNNNNNNNNNNNNNCNNNNNNCNNCCCNNCANNNNNNNCNNNNNNNNNNNNNNNNNNNNNTCNCTNCNCNCCCCNCCCNNNNNNNG', 'qual': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 'sample': 'D11F', 'sample_well': 'C5', 'dye': None, 'polymer': None, 'machine_model': '310 ', 'run_start': '2009-02-19 01:19:30', 'run_finish': '2009-02-19 04:04:15', }, } test_data_fake = { 'fake': { 'path': ['Abi', 'fake.ab1'], } } def open_files(test_array): for trace in test_array: test_array[trace]['handle'] = open(join(*test_array[trace]['path']), 'rb') def open_files_wrong_mode(test_array): for trace in test_array: test_array[trace]['handle'] = open(join(*test_array[trace]['path'])) def close_files(test_array): for trace in test_array: test_array[trace]['handle'].close() class TestAbi(unittest.TestCase): def setUp(self): open_files(test_data) def tearDown(self): close_files(test_data) def test_file_type(self): """Test if filetype is ABIF.""" for trace in test_data: self.assertEqual(test_data[trace]['handle'].read(4), _as_bytes('ABIF')) def test_seqrecord(self): """Test if the extracted seqrecords data are equal to expected values.""" for trace in test_data: record = SeqIO.read(test_data[trace]['handle'], 'abi') self.assertEqual(basename(test_data[trace]["path"][-1]).replace('.ab1', ''), record.name) self.assertEqual(test_data[trace]['seq'], str(record.seq)) self.assertEqual(test_data[trace]['qual'], record.letter_annotations['phred_quality']) self.assertEqual(test_data[trace]['sample'], record.id) self.assertEqual(test_data[trace]['sample_well'], record.annotations['sample_well']) self.assertEqual(test_data[trace]['machine_model'], record.annotations['machine_model']) self.assertEqual(test_data[trace]['run_start'], record.annotations['run_start']) self.assertEqual(test_data[trace]['run_finish'], record.annotations['run_finish']) def test_trim(self): """Test if trim works.""" for trace in test_data: record = SeqIO.read(test_data[trace]['handle'], 'abi-trim') if trace != 'data_empty': self.assertNotEqual(str(record.seq), test_data[trace]['seq']) self.assertTrue(str(record.seq) in test_data[trace]['seq']) else: self.assertEqual(str(record.seq), test_data[trace]['seq']) class TestAbiWrongMode(unittest.TestCase): def test_file_mode(self): """Test if exception is raised if file is not opened in 'rb' mode.""" open_files_wrong_mode(test_data) for trace in test_data: self.assertRaises(ValueError, SeqIO.read, test_data[trace]['handle'], 'abi') close_files(test_data) class TestAbiFake(unittest.TestCase): def test_file_type(self): """Test if error is raised if filetype is not ABIF.""" open_files(test_data_fake) for trace in test_data_fake: self.assertRaises(IOError, SeqIO.read, test_data_fake[trace]['handle'], 'abi') close_files(test_data_fake) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity = 2) unittest.main(testRunner=runner)