# Copyright 2022 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 Align.bed module.""" import unittest import os from io import StringIO from Bio import Align from Bio.Align import Alignment from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio import SeqIO from Bio import BiopythonExperimentalWarning import numpy class TestAlign_dna_rna(unittest.TestCase): # The BED file dna_rna.bed was generated using this command: # pslToBed dna_rna.psl dna_rna.bed def setUp(self): data = {} records = SeqIO.parse("Blat/dna.fa", "fasta") for record in records: name, start_end = record.id.split(":") assert name == "chr3" start, end = start_end.split("-") start = int(start) end = int(end) sequence = str(record.seq) assert len(sequence) == end - start data[start] = sequence self.dna = Seq(data, length=198295559) # hg38 chr3 records = SeqIO.parse("Blat/rna.fa", "fasta") self.rna = {record.id: record.seq for record in records} def test_reading(self): """Test parsing dna_rna.bed.""" path = "Blat/dna_rna.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 5407)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_111921.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[48663767, 48663813, 48665640, 48665722, 48669098, 48669174], [ 0, 46, 46, 128, 128, 204]]) # fmt: on ) ) alignment.target.seq = self.dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( numpy.array_equal( alignment.substitutions, # fmt: off # flake8: noqa numpy.array([[53., 0., 0., 0., 0., 0., 0., 0.], [ 0., 35., 0., 0., 0., 0., 0., 0.], [ 0., 0., 50., 0., 0., 0., 0., 0.], [ 0., 0., 0., 27., 0., 0., 0., 0.], [ 9., 0., 0., 0., 0., 0., 0., 0.], [ 0., 7., 0., 0., 0., 0., 0., 0.], [ 0., 0., 16., 0., 0., 0., 0., 0.], [ 0., 0., 0., 7., 0., 0., 0., 0.], ]) ) ) self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt") self.assertEqual( format(alignment, "bed"), """\ chr3 48663767 48669174 NR_111921.1 1000 + 48663767 48669174 0 3 46,82,76, 0,1873,5331, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 1711)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606], [ 181, 118, 118, 43, 43, 0]]) # fmt: on ) ) alignment.target.seq = self.dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( numpy.array_equal( alignment.substitutions, # fmt: off # flake8: noqa numpy.array([[36., 0., 0., 0., 0., 0., 0., 0.], [ 0., 40., 0., 0., 0., 0., 0., 0.], [ 0., 0., 57., 0., 0., 0., 0., 0.], [ 0., 0., 0., 42., 0., 0., 0., 0.], [ 2., 0., 0., 0., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0., 0., 0., 0.], [ 0., 0., 3., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0., 0.], ]) ) ) self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt") self.assertEqual( format(alignment, "bed"), """\ chr3 42530895 42532606 NR_046654.1 1000 - 42530895 42532606 0 3 63,75,43, 0,1125,1668, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 972) self.assertEqual(alignment.shape, (2, 5407)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_111921.1_modified") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[48663767, 48663795, 48663796, 48663813, 48665640, 48665716, 48665722, 48669098, 48669174], [ 0, 28, 28, 45, 45, 121, 127, 127, 203]]) # fmt: on ) ) # The modified RNAs have gaps in their sequence. As this information is # not stored in a BED file, we cannot calculate the substitution matrix. self.assertEqual( format(alignment, "bed"), """\ chr3 48663767 48669174 NR_111921.1_modified 972 + 48663767 48669174 0 5 28,17,76,6,76, 0,29,1873,1949,5331, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 978) self.assertEqual(alignment.shape, (2, 1711)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1_modified") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[42530895, 42530922, 42530958, 42532020, 42532037, 42532039, 42532095, 42532563, 42532606], [ 179, 152, 116, 116, 99, 99, 43, 43, 0]]) # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr3 42530895 42532606 NR_046654.1_modified 978 - 42530895 42532606 0 5 27,36,17,56,43, 0,27,1125,1144,1668, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing(self): """Test writing the alignments in dna_rna.bed.""" path = "Blat/dna_rna.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 4) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_dna(unittest.TestCase): def test_reading_psl_34_001(self): """Test parsing psl_34_001.bed.""" path = "Blat/psl_34_001.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[61646095, 61646111], [ 0, 16]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 61646095 61646111 hg19_dna 1000 + 61646095 61646111 0 1 16, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 10271783 10271816 hg19_dna 1000 + 10271783 10271816 0 1 33, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[53575980, 53575997], [ 17, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 53575980 53575997 hg19_dna 1000 - 53575980 53575997 0 1 17, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[85737865, 85737906], [ 0, 41]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[95160479, 95160520], [ 0, 41]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[42144400, 42144436], [ 0, 36]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[23891310, 23891349], [ 0, 39]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[43252217, 43252245], [ 0, 28]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[61700837, 61700871], [ 0, 34]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[48997405, 48997442], [ 37, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[120641740, 120641776], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[54017130, 54017169], [ 39, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[553742, 553781], [ 39, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[99388555, 99388591], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[112178171, 112178196], [ 25, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[39368490, 39368526], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[220325687, 220325721], [ 34, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_001(self): """Test writing the alignments in psl_34_001.bed.""" path = "Blat/psl_34_001.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 22) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_003(self): """Test parsing psl_34_003.bed.""" path = "Blat/psl_34_003.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[61646095, 61646111], [ 0, 16]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 61646095 61646111 hg18_dna 1000 + 61646095 61646111 0 1 16, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 10271783 10271816 hg18_dna 1000 + 10271783 10271816 0 1 33, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[53575980, 53575997], [ 17, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 53575980 53575997 hg18_dna 1000 - 53575980 53575997 0 1 17, 0, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_003(self): """Test writing the alignments in psl_34_003.bed.""" path = "Blat/psl_34_003.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 3) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_004(self): """Test parsing psl_34_004.bed.""" path = "Blat/psl_34_004.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[85737865, 85737906], [ 0, 41]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[95160479, 95160520], [ 0, 41]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[42144400, 42144436], [ 0, 36]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[23891310, 23891349], [ 0, 39]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[43252217, 43252245], [ 0, 28]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[61700837, 61700871], [ 0, 34]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[48997405, 48997442], [ 37, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[120641740, 120641776], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[54017130, 54017169], [ 39, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[553742, 553781], [ 39, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[99388555, 99388591], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[112178171, 112178196], [ 25, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[39368490, 39368526], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[220325687, 220325721], [ 34, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_004(self): """Test writing the alignments in psl_34_004.bed.""" path = "Blat/psl_34_004.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 19) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_005(self): """Test parsing psl_34_005.bed.""" path = "Blat/psl_34_005.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[61646095, 61646111], [ 0, 16]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 61646095 61646111 hg19_dna 1000 + 61646095 61646111 0 1 16, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 10271783 10271816 hg19_dna 1000 + 10271783 10271816 0 1 33, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[53575980, 53575997], [ 17, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 53575980 53575997 hg19_dna 1000 - 53575980 53575997 0 1 17, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[85737865, 85737906], [ 0, 41]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[95160479, 95160520], [ 0, 41]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[42144400, 42144436], [ 0, 36]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[23891310, 23891349], [ 0, 39]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[43252217, 43252245], [ 0, 28]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[61700837, 61700871], [ 0, 34]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[48997405, 48997442], [ 37, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[120641740, 120641776], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[54017130, 54017169], [ 39, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[553742, 553781], [ 39, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[99388555, 99388591], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[112178171, 112178196], [ 25, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off numpy.array([[39368490, 39368526], [ 36, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[220325687, 220325721], [ 34, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_005(self): """Test writing the alignments in psl_34_005.bed.""" path = "Blat/psl_34_005.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 22) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_dnax_prot(unittest.TestCase): def test_reading_psl_35_001(self): """Test parsing psl_35_001.bed.""" path = "Blat/psl_35_001.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[75566694, 75566850], [ 0, 156]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 75566694 75566850 CAG33136.1 1000 + 75566694 75566850 0 1 156, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[75560749, 75560881], [ 0, 132]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 75560749 75560881 CAG33136.1 1000 + 75560749 75560881 0 1 132, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 986) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[75549820, 75549865, 75567225, 75567312], [ 0, 45, 45, 132]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 75549820 75567312 CAG33136.1 986 + 75549820 75567312 0 2 45,87, 0,17405, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[75604767, 75604827, 75605728, 75605809], [ 0, 60, 60, 141]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 75604767 75605809 CAG33136.1 1000 + 75604767 75605809 0 2 60,81, 0,961, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[75594914, 75594989], [ 0, 75]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 75594914 75594989 CAG33136.1 1000 + 75594914 75594989 0 1 75, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[75569459, 75569507], [ 0, 48]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr13 75569459 75569507 CAG33136.1 1000 + 75569459 75569507 0 1 48, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 530) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[41260685, 41260787], [ 0, 102]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 41260685 41260787 CAG33136.1 530 + 41260685 41260787 0 1 102, 0, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 166) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[41257605, 41257731, 41263227, 41263290], [ 0, 126, 126, 189]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ chr4 41257605 41263290 CAG33136.1 166 + 41257605 41263290 0 2 126,63, 0,5622, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_35_001(self): """Test writing the alignments in psl_35_001.bed.""" path = "Blat/psl_35_001.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 8) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_35_002(self): """Test parsing psl_35_002.bed.""" path = "Blat/psl_35_002.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 972) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI537979") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[9712654, 9712786, 9715941, 9716097, 9716445, 9716532, 9718374, 9718422, 9739264, 9739339, 9743706, 9743766, 9744511, 9744592], [ 0, 132, 132, 288, 288, 375, 375, 423, 423, 498, 498, 558, 558, 639]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ KI537979 9712654 9744592 CAG33136.1 972 + 9712654 9744592 0 7 132,156,87,48,75,60,81, 0,3287,3791,5720,26610,31052,31857, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 792) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI538594") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[2103463, 2103523, 2103522, 2104149], [ 0, 60, 60, 687]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ KI538594 2103463 2104149 CAG33136.1 792 + 2103463 2104149 0 2 60,627, 0,59, """, ) alignment = next(alignments) self.assertEqual(alignment.score, 902) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI537194") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[20872390, 20872471, 20872472, 20873021], [ 630, 549, 549, 0]]), # fmt: on ) ) self.assertEqual( format(alignment, "bed"), """\ KI537194 20872390 20873021 CAG33136.1 902 - 20872390 20873021 0 2 81,549, 0,82, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_35_002(self): """Test writing the alignments in psl_35_002.bed.""" path = "Blat/psl_35_002.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 3) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_bed12(unittest.TestCase): def test_reading(self): """Test parsing alignments in file formats BED3 through BED12.""" for bedN in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.bed" % bedN path = os.path.join("Blat", filename) alignments = Align.parse(path, "bed") alignment = next(alignments) if bedN >= 5: self.assertEqual(alignment.score, 960, msg=filename) self.assertEqual(alignment.shape, (2, 4000), msg=filename) self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=filename ) self.assertLess( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename ) self.assertEqual(len(alignment), 2, msg=filename) self.assertIs(alignment.sequences[0], alignment.target, msg=filename) self.assertIs(alignment.sequences[1], alignment.query, msg=filename) self.assertEqual(alignment.target.id, "chr22", msg=filename) if bedN >= 4: self.assertEqual(alignment.query.id, "mRNA1", msg=filename) else: self.assertIsNone(alignment.query.id, msg=filename) if bedN == 12: self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[1000, 1567, 4512, 5000], [ 0, 567, 567, 1055]]), # fmt: on ), msg=filename, ) else: self.assertTrue( numpy.array_equal( alignment.coordinates, numpy.array([[1000, 5000], [0, 4000]]), ), msg=filename, ) if bedN >= 7: self.assertEqual(alignment.thickStart, 1200, msg=filename) if bedN >= 8: self.assertEqual(alignment.thickEnd, 4900, msg=filename) if bedN >= 9: self.assertEqual(alignment.itemRgb, "255,0,0", msg=filename) words = [ "chr22", "1000", "5000", "mRNA1", "960", "+", "1200", "4900", "255,0,0", "2", "567,488,", "0,3512,", ] self.assertEqual( alignment.format("bed", bedN), "\t".join(words[:bedN]) + "\n" ) alignment = next(alignments) if bedN >= 5: self.assertEqual(alignment.score, 900, msg=filename) self.assertEqual(alignment.shape, (2, 4000), msg=filename) self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=filename ) if bedN >= 6: self.assertGreater( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename, ) else: self.assertLess( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename, ) self.assertEqual(len(alignment), 2, msg=filename) self.assertIs(alignment.sequences[0], alignment.target, msg=filename) self.assertIs(alignment.sequences[1], alignment.query, msg=filename) self.assertEqual(alignment.target.id, "chr22", msg=filename) if bedN >= 4: self.assertEqual(alignment.query.id, "mRNA2", msg=filename) else: self.assertIsNone(alignment.query.id, msg=filename) if bedN == 12: self.assertTrue( numpy.array_equal( alignment.coordinates, # fmt: off # flake8: noqa numpy.array([[2000, 2433, 5601, 6000], [ 832, 399, 399, 0]]) # fmt: on ), msg=filename, ) elif bedN >= 6: self.assertTrue( numpy.array_equal( alignment.coordinates, numpy.array([[2000, 6000], [4000, 0]]), ), msg=filename, ) else: self.assertTrue( numpy.array_equal( alignment.coordinates, numpy.array([[2000, 6000], [0, 4000]]), ), msg=filename, ) if bedN >= 7: self.assertEqual(alignment.thickStart, 2300, msg=filename) if bedN >= 8: self.assertEqual(alignment.thickEnd, 5960, msg=filename) if bedN >= 9: self.assertEqual(alignment.itemRgb, "0,255,0", msg=filename) words = [ "chr22", "2000", "6000", "mRNA2", "900", "-", "2300", "5960", "0,255,0", "2", "433,399,", "0,3601,", ] self.assertEqual( alignment.format("bed", bedN), "\t".join(words[:bedN]) + "\n" ) with self.assertRaises(StopIteration) as cm: next(alignments) self.fail(f"More than two alignments reported in {filename}") def test_writing(self): """Test writing the alignments in bed12.bed as BED3 through BED12.""" for bedN in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.bed" % bedN path = os.path.join("Blat", filename) with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed", bedN=bedN) self.assertEqual(n, 2, msg=filename) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data, msg=filename) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)