# Copyright 2021 by Michiel de Hoon. All rights reserved. # # 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. """Tests for Bio.Align.nexus module.""" import unittest from io import StringIO from Bio import Align try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.nexus." ) from None class TestNexusReading(unittest.TestCase): def check_reading_writing(self, path): alignments = Align.parse(path, "nexus") stream = StringIO() n = Align.write(alignments, stream, "nexus") self.assertEqual(n, 1) alignments = Align.parse(path, "nexus") alignments = list(alignments) alignment = alignments[0] stream.seek(0) saved_alignments = Align.parse(stream, "nexus") saved_alignments = list(saved_alignments) self.assertEqual(len(alignments), len(saved_alignments)) saved_alignment = saved_alignments[0] for i, (sequence, saved_sequence) in enumerate( zip(alignment.sequences, saved_alignment.sequences) ): self.assertEqual(sequence.id, saved_sequence.id) self.assertEqual(sequence.seq, saved_sequence.seq) self.assertEqual(sequence.annotations, saved_sequence.annotations) self.assertEqual(alignment[i], saved_alignment[i]) self.assertTrue( np.array_equal(alignment.coordinates, saved_alignment.coordinates) ) def test_nexus1(self): path = "Nexus/test_Nexus_input.nex" alignments = Align.parse(path, "nexus") self.check_nexus1(alignments) alignments = iter(alignments) self.check_nexus1(alignments) with Align.parse(path, "nexus") as alignments: self.check_nexus1(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "nexus") as alignments: pass with self.assertRaises(AttributeError): alignments._stream self.check_reading_writing(path) def check_nexus1(self, alignments): alignment = next(alignments) self.assertEqual(len(alignment), 9) self.assertEqual(alignment.shape, (9, 46)) self.assertEqual(alignment.sequences[0].id, "t1") self.assertEqual(alignment.sequences[1].id, "t2 the name") self.assertEqual(alignment.sequences[2].id, "isn'that [a] strange name?") self.assertEqual( alignment.sequences[3].id, "one should be punished, for (that)!" ) self.assertEqual(alignment.sequences[4].id, "t5") self.assertEqual(alignment.sequences[5].id, "t6") self.assertEqual(alignment.sequences[6].id, "t7") self.assertEqual(alignment.sequences[7].id, "t8") self.assertEqual(alignment.sequences[8].id, "t9") self.assertEqual(alignment.sequences[0].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[1].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[2].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[3].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[4].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[5].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[6].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[7].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[8].annotations, {"molecule_type": "DNA"}) self.assertEqual( alignment.sequences[0].seq, "ACGTcgtgtgtgctctttacgtgtgtgctcttt" ) self.assertEqual(alignment.sequences[1].seq, "ACGcTcgtgtctttacacgtgtcttt") self.assertEqual(alignment.sequences[2].seq, "ACcGcTcgtgtgtgctacacacgtgtgtgct") self.assertEqual(alignment.sequences[3].seq, "ACGT") self.assertEqual( alignment.sequences[4].seq, "AC?GT?acgt???????????acgt????????" ) self.assertEqual( alignment.sequences[5].seq, "AcCaGtTc?aaaaaaaaaaacgactac?aaaaaaaaaa" ) self.assertEqual( alignment.sequences[6].seq, "A?CGgTgggggggggggggg???gggggggggggggggg" ) self.assertEqual( alignment.sequences[7].seq, "AtCtGtTtttttttttttt??ttttttttttttttttttt??" ) self.assertEqual( alignment.sequences[8].seq, "cccccccccccccccccccNcccccccccccccccccccccNcc" ) self.assertEqual( str(alignment), """\ t1 0 A-C-G-Tcgtgtgtgctct-t-t------acgtgtgtgctct-t-t 33 t2 the na 0 A-C-GcTcgtg-----tct-t-t----acacgtg-----tct-t-t 26 isn'that 0 A-CcGcTcgtgtgtgct--------acacacgtgtgtgct------ 31 one shoul 0 A-C-G-T--------------------------------------- 4 t5 0 A-C?G-T?-acgt??-???-???--??---?-acgt??-???-??? 33 t6 0 AcCaGtTc?--aaaaaaaa-a-aacgactac?--aaaaaaaa-a-a 38 t7 0 A?C-GgTgggggggggggg-g-g??--?gggggggggggggg-g-g 39 t8 0 AtCtGtTtttttttttttt-?-?ttttttttttttttttttt-?-? 42 t9 0 cccccccccccccccccccNc-ccccccccccccccccccccNc-c 44 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 1, 1, 2, 2, 3, 3, 4, 5, 6, 8, 12, 13, 14, 16, 16, 17, 17, 18, 18, 18, 18, 19, 20, 21, 23, 27, 28, 29, 31, 31, 32, 32, 33], [ 0, 1, 1, 2, 2, 3, 4, 5, 6, 7, 9, 9, 9, 10, 12, 12, 13, 13, 14, 14, 14, 16, 17, 18, 19, 21, 21, 21, 22, 24, 24, 25, 25, 26], [ 0, 1, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 16, 16, 16, 16, 16, 16, 18, 20, 21, 22, 23, 25, 29, 30, 31, 31, 31, 31, 31, 31], [ 0, 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4], [ 0, 1, 1, 2, 3, 4, 4, 5, 6, 6, 8, 12, 12, 13, 15, 15, 16, 17, 18, 18, 20, 20, 20, 21, 21, 23, 27, 27, 28, 30, 30, 31, 32, 33], [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 9, 13, 14, 15, 17, 17, 18, 18, 19, 21, 23, 25, 26, 27, 28, 28, 32, 33, 34, 36, 36, 37, 37, 38], [ 0, 1, 2, 3, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 18, 18, 19, 19, 20, 22, 22, 24, 25, 26, 27, 29, 33, 34, 35, 37, 37, 38, 38, 39], [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 19, 19, 20, 20, 21, 23, 25, 27, 28, 29, 30, 32, 36, 37, 38, 40, 40, 41, 41, 42], [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 19, 20, 21, 21, 22, 24, 26, 28, 29, 30, 31, 33, 37, 38, 39, 41, 42, 43, 43, 44]]) # fmt: on ) ) self.assertEqual( alignment[0], "A-C-G-Tcgtgtgtgctct-t-t------acgtgtgtgctct-t-t", ) self.assertEqual( alignment[1], "A-C-GcTcgtg-----tct-t-t----acacgtg-----tct-t-t", ) self.assertEqual(alignment[2], "A-CcGcTcgtgtgtgct--------acacacgtgtgtgct------") self.assertEqual(alignment[3], "A-C-G-T---------------------------------------") self.assertEqual(alignment[4], "A-C?G-T?-acgt??-???-???--??---?-acgt??-???-???") self.assertEqual(alignment[5], "AcCaGtTc?--aaaaaaaa-a-aacgactac?--aaaaaaaa-a-a") self.assertEqual(alignment[6], "A?C-GgTgggggggggggg-g-g??--?gggggggggggggg-g-g") self.assertEqual(alignment[7], "AtCtGtTtttttttttttt-?-?ttttttttttttttttttt-?-?") self.assertEqual(alignment[8], "cccccccccccccccccccNc-ccccccccccccccccccccNc-c") self.assertEqual( format(alignment, "nexus"), """\ #NEXUS begin data; dimensions ntax=9 nchar=46; format datatype=dna missing=? gap=-; matrix t1 A-C-G-Tcgtgtgtgctct-t-t------acgtgtgtgctct-t-t 't2 the name' A-C-GcTcgtg-----tct-t-t----acacgtg-----tct-t-t 'isn''that [a] strange name?' A-CcGcTcgtgtgtgct--------acacacgtgtgtgct------ 'one should be punished, for (that)!' A-C-G-T--------------------------------------- t5 A-C?G-T?-acgt??-???-???--??---?-acgt??-???-??? t6 AcCaGtTc?--aaaaaaaa-a-aacgactac?--aaaaaaaa-a-a t7 A?C-GgTgggggggggggg-g-g??--?gggggggggggggg-g-g t8 AtCtGtTtttttttttttt-?-?ttttttttttttttttttt-?-? t9 cccccccccccccccccccNc-ccccccccccccccccccccNc-c ; end; """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', '-', 'C', '-', 'G', '-', 'T', 'c', 'g', 't', 'g', 't', 'g', 't', 'g', 'c', 't', 'c', 't', '-', 't', '-', 't', '-', '-', '-', '-', '-', '-', 'a', 'c', 'g', 't', 'g', 't', 'g', 't', 'g', 'c', 't', 'c', 't', '-', 't', '-', 't'], ['A', '-', 'C', '-', 'G', 'c', 'T', 'c', 'g', 't', 'g', '-', '-', '-', '-', '-', 't', 'c', 't', '-', 't', '-', 't', '-', '-', '-', '-', 'a', 'c', 'a', 'c', 'g', 't', 'g', '-', '-', '-', '-', '-', 't', 'c', 't', '-', 't', '-', 't'], ['A', '-', 'C', 'c', 'G', 'c', 'T', 'c', 'g', 't', 'g', 't', 'g', 't', 'g', 'c', 't', '-', '-', '-', '-', '-', '-', '-', '-', 'a', 'c', 'a', 'c', 'a', 'c', 'g', 't', 'g', 't', 'g', 't', 'g', 'c', 't', '-', '-', '-', '-', '-', '-'], ['A', '-', 'C', '-', 'G', '-', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['A', '-', 'C', '?', 'G', '-', 'T', '?', '-', 'a', 'c', 'g', 't', '?', '?', '-', '?', '?', '?', '-', '?', '?', '?', '-', '-', '?', '?', '-', '-', '-', '?', '-', 'a', 'c', 'g', 't', '?', '?', '-', '?', '?', '?', '-', '?', '?', '?'], ['A', 'c', 'C', 'a', 'G', 't', 'T', 'c', '?', '-', '-', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', '-', 'a', '-', 'a', 'a', 'c', 'g', 'a', 'c', 't', 'a', 'c', '?', '-', '-', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', '-', 'a', '-', 'a'], ['A', '?', 'C', '-', 'G', 'g', 'T', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', '-', 'g', '-', 'g', '?', '?', '-', '-', '?', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', 'g', '-', 'g', '-', 'g'], ['A', 't', 'C', 't', 'G', 't', 'T', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', '-', '?', '-', '?', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', '-', '?', '-', '?'], ['c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'N', 'c', '-', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'N', 'c', '-', 'c']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_nexus2(self): path = "Nexus/codonposset.nex" alignments = Align.parse(path, "nexus") alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 22)) self.assertEqual(alignment.sequences[0].id, "Aegotheles") self.assertEqual(alignment.sequences[1].id, "Aerodramus") self.assertEqual(alignment.sequences[0].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[1].annotations, {"molecule_type": "DNA"}) self.assertEqual(alignment.sequences[0].seq, "AAAAAGGCATTGTGGTGGGAAT") self.assertEqual(alignment.sequences[1].seq, "?????????TTGTGGTGGGAAT") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 22], [0, 22]])) ) self.assertEqual(alignment[0], "AAAAAGGCATTGTGGTGGGAAT") self.assertEqual(alignment[1], "?????????TTGTGGTGGGAAT") self.assertEqual( str(alignment), """\ Aegothele 0 AAAAAGGCATTGTGGTGGGAAT 22 0 .........||||||||||||| 22 Aerodramu 0 ?????????TTGTGGTGGGAAT 22 """, ) self.assertEqual( format(alignment, "nexus"), """\ #NEXUS begin data; dimensions ntax=2 nchar=22; format datatype=dna missing=? gap=-; matrix Aegotheles AAAAAGGCATTGTGGTGGGAAT Aerodramus ?????????TTGTGGTGGGAAT ; end; """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'A', 'A', 'A', 'A', 'G', 'G', 'C', 'A', 'T', 'T', 'G', 'T', 'G', 'G', 'T', 'G', 'G', 'G', 'A', 'A', 'T'], ['?', '?', '?', '?', '?', '?', '?', '?', '?', 'T', 'T', 'G', 'T', 'G', 'G', 'T', 'G', 'G', 'G', 'A', 'A', 'T']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) self.check_reading_writing(path) class TestNexusBasic(unittest.TestCase): def test_empty(self): import io stream = io.StringIO() with self.assertRaisesRegex(ValueError, "Empty file."): Align.parse(stream, "nexus") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)