# 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.bigpsl module.""" import tempfile import unittest from Bio import Align from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqFeature import BeforePosition from Bio.SeqFeature import CompoundLocation from Bio.SeqFeature import ExactPosition from Bio.SeqFeature import SeqFeature from Bio.SeqFeature import SimpleLocation try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.bigpsl." ) from None class TestAlign_declaration(unittest.TestCase): def test_declaration(self): with open("Blat/bigPsl.as") as stream: declaration = stream.read() self.assertEqual(str(Align.bigpsl.declaration), declaration) class TestAlign_dna_rna(unittest.TestCase): # The bigPsl file dna_rna.psl.bb was generated using these commands: # pslToBigPsl dna_rna.psl stdout | sort -k1,1 -k2,2n > dna_rna.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as dna_rna.bigPslInput hg38.chrom.sizes dna_rna.psl.bb 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 = data records = SeqIO.parse("Blat/rna.fa", "fasta") self.rna = {record.id: record.seq for record in records} self.path = "Blat/dna_rna.psl.bb" def test_reading(self): """Test parsing dna_rna.psl.bb.""" alignments = Align.parse(self.path, "bigpsl") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(self.path, "bigpsl") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(self.path, "bigpsl") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def test_writing(self): """Test writing dna_rna.psl.bb.""" alignments = Align.parse(self.path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl") output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 1) self.assertEqual(alignments.targets[0].id, "chr3") self.assertEqual(len(alignments.targets[0]), 198295559) self.assertEqual(len(alignments), 4) alignment = next(alignments) self.assertEqual(alignment.matches, 175) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 6) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 42530895) self.assertEqual(alignment.thickEnd, 42532606) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 181) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606], [ 181, 118, 118, 43, 43, 0]]) # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.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") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 181: identities = 175, mismatches = 6. gaps = 1530: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1530: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1530: open_internal_deletions = 2, extend_internal_deletions = 1528; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1530) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1530) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1530) self.assertEqual(counts.gaps, 1530) self.assertEqual(counts.aligned, 181) self.assertEqual(counts.identities, 175) self.assertEqual(counts.mismatches, 6) alignment = next(alignments) self.assertEqual(alignment.matches, 172) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 6) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 42530895) self.assertEqual(alignment.thickEnd, 42532606) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 1714)) 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.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 190) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530922, 42530922, 42530958, 42532020, 42532037, 42532039, 42532095, 42532563, 42532606], [ 185, 158, 155, 119, 119, 102, 102, 46, 46, 3], ]) # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.array([[34., 0., 0., 1., 0., 0., 0., 0.], [ 0., 40., 0., 0., 0., 0., 0., 0.], [ 0., 0., 57., 0., 0., 0., 0., 0.], [ 0., 0., 0., 41., 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") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet if c != "X" ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 179: identities = 172, mismatches = 7. gaps = 1535: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1535: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 1532: open_internal_deletions = 3, extend_internal_deletions = 1529; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 1532) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1535) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 1532) self.assertEqual(counts.gaps, 1535) self.assertEqual(counts.aligned, 179) self.assertEqual(counts.identities, 172) self.assertEqual(counts.mismatches, 7) alignment = next(alignments) self.assertEqual(alignment.matches, 165) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 39) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 48663767) self.assertEqual(alignment.thickEnd, 48669174) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 216) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array( [[48663767, 48663813, 48665640, 48665722, 48669098, 48669174], [ 0, 46, 46, 128, 128, 204]]), # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target.seq)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.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") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 204: identities = 165, mismatches = 39. gaps = 5203: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5203: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 5203: open_internal_deletions = 2, extend_internal_deletions = 5201; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 5203) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5203) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5203) self.assertEqual(counts.gaps, 5203) self.assertEqual(counts.aligned, 204) self.assertEqual(counts.identities, 165) self.assertEqual(counts.mismatches, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 162) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 39) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 48663767) self.assertEqual(alignment.thickEnd, 48669174) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 5409)) 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.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 220) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48663767, 48663795, 48663796, 48663813, 48665640, 48665716, 48665716, 48665722, 48669098, 48669174], [ 3, 31, 31, 48, 48, 124, 126, 132, 132, 208] ]) # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.array([[53., 0., 0., 0., 0., 0., 0., 0.], [ 0., 34., 0., 0., 0., 0., 0., 0.], [ 0., 2., 48., 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") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet if c != "X" ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 203: identities = 162, mismatches = 41. gaps = 5206: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5206: internal_insertions = 2: open_internal_insertions = 1, extend_internal_insertions = 1; internal_deletions = 5204: open_internal_deletions = 3, extend_internal_deletions = 5201; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 2) self.assertEqual(counts.internal_deletions, 5204) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5206) self.assertEqual(counts.insertions, 2) self.assertEqual(counts.deletions, 5204) self.assertEqual(counts.gaps, 5206) self.assertEqual(counts.aligned, 203) self.assertEqual(counts.identities, 162) self.assertEqual(counts.mismatches, 41) self.assertRaises(StopIteration, next, alignments) class TestAlign_dna(unittest.TestCase): queries = { record.id: record.seq for record in SeqIO.parse("Blat/fasta_34.fa", "fasta") } def test_reading_psl_34_001(self): """Test parsing psl_34_001.psl.bb.""" # The bigPsl file psl_34_001.psl.bb was generated using these commands: # pslToBigPsl -fa=fasta_34.fa psl_34_001.psl stdout | sort -k1,1 -k2,2n > psl_34_001.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as psl_34_001.bigPslInput hg19.chrom.sizes psl_34_001.psl.bb path = "Blat/psl_34_001.psl.bb" alignments = Align.parse(path, "bigpsl") self.check_psl_34_001(alignments) def test_writing_psl_34_001(self): """Test writing psl_34_001.psl.bb.""" path = "Blat/psl_34_001.psl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", fa=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_psl_34_001(alignments) def check_psl_34_001(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 10) self.assertEqual(alignments.targets[0].id, "chr1") self.assertEqual(len(alignments.targets[0]), 249250621) self.assertEqual(alignments.targets[1].id, "chr10") self.assertEqual(len(alignments.targets[1]), 135534747) self.assertEqual(alignments.targets[2].id, "chr13") self.assertEqual(len(alignments.targets[2]), 115169878) self.assertEqual(alignments.targets[3].id, "chr18") self.assertEqual(len(alignments.targets[3]), 78077248) self.assertEqual(alignments.targets[4].id, "chr19") self.assertEqual(len(alignments.targets[4]), 59128983) self.assertEqual(alignments.targets[5].id, "chr2") self.assertEqual(len(alignments.targets[5]), 243199373) self.assertEqual(alignments.targets[6].id, "chr22") self.assertEqual(len(alignments.targets[6]), 51304566) self.assertEqual(alignments.targets[7].id, "chr4") self.assertEqual(len(alignments.targets[7]), 191154276) self.assertEqual(alignments.targets[8].id, "chr8") self.assertEqual(len(alignments.targets[8]), 146364022) self.assertEqual(alignments.targets[9].id, "chr9") self.assertEqual(len(alignments.targets[9]), 141213431) self.assertEqual(len(alignments), 22) alignment = next(alignments) self.assertEqual(alignment.matches, 50) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 1207056) self.assertEqual(alignment.thickEnd, 1207106) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 10271783) self.assertEqual(alignment.thickEnd, 10271816) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 39368490) self.assertEqual(alignment.thickEnd, 39368526) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 31) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 61700837) self.assertEqual(alignment.thickEnd, 61700871) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 220325687) self.assertEqual(alignment.thickEnd, 220325721) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 99388555) self.assertEqual(alignment.thickEnd, 99388591) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 24) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 112178171) self.assertEqual(alignment.thickEnd, 112178196) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 52759147) self.assertEqual(alignment.thickEnd, 52759198) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 54)) 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.assertEqual(len(alignment.target.seq), 115169878) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759160, 52759198], [ 1, 8, 8, 11, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 9: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 9: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 9) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 9) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 23891310) self.assertEqual(alignment.thickEnd, 23891349) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 27) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 43252217) self.assertEqual(alignment.thickEnd, 43252245) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.matches, 36) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 553742) self.assertEqual(alignment.thickEnd, 553781) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 34) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 35483340) self.assertEqual(alignment.thickEnd, 35483510) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 10, 35, 35, 46]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 54017130) self.assertEqual(alignment.thickEnd, 54017169) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 17) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 53575980) self.assertEqual(alignment.thickEnd, 53575997) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 120641740) self.assertEqual(alignment.thickEnd, 120641776) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 43) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 183925984) self.assertEqual(alignment.thickEnd, 183926028) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 48)) 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183925990, 183926028], [ 1, 7, 11, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 4: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 4: internal_insertions = 4: open_internal_insertions = 1, extend_internal_insertions = 3; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 4) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 4) self.assertEqual(counts.insertions, 4) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 4) self.assertEqual(counts.aligned, 44) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 42144400) self.assertEqual(alignment.thickEnd, 42144436) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 48997405) self.assertEqual(alignment.thickEnd, 48997442) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) self.assertEqual(alignment.matches, 28) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 37558157) self.assertEqual(alignment.thickEnd, 37558191) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 44)) 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.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558173, 37558191], [ 49, 39, 39, 29, 11]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 16: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 16: internal_insertions = 10: open_internal_insertions = 1, extend_internal_insertions = 9; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 10) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 16) self.assertEqual(counts.insertions, 10) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 16) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 61646095) self.assertEqual(alignment.thickEnd, 61646111) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) self.assertEqual(alignment.matches, 41) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 95160479) self.assertEqual(alignment.thickEnd, 95160520) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 146364022) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.matches, 38) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 85737865) self.assertEqual(alignment.thickEnd, 85737906) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 141213431) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) self.assertRaises(StopIteration, next, alignments) def test_reading_psl_34_003(self): """Test parsing psl_34_003.psl.bb.""" # The bigPsl file psl_34_003.psl.bb was generated using these commands: # pslToBigPsl -fa=fasta_34.fa psl_34_003.psl stdout | sort -k1,1 -k2,2n > psl_34_003.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as psl_34_003.bigPslInput hg19.chrom.sizes psl_34_003.psl.bb path = "Blat/psl_34_003.psl.bb" alignments = Align.parse(path, "bigpsl") self.check_psl_34_003(alignments) def test_writing_psl_34_003(self): """Test writing psl_34_003.psl.bb.""" path = "Blat/psl_34_003.psl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", fa=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_psl_34_003(alignments) def check_psl_34_003(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 3) self.assertEqual(alignments.targets[0].id, "chr1") self.assertEqual(len(alignments.targets[0]), 249250621) self.assertEqual(alignments.targets[1].id, "chr2") self.assertEqual(len(alignments.targets[1]), 243199373) self.assertEqual(alignments.targets[2].id, "chr4") self.assertEqual(len(alignments.targets[2]), 191154276) self.assertEqual(len(alignments), 3) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 10271783) self.assertEqual(alignment.thickEnd, 10271816) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) self.assertEqual(alignment.matches, 17) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 53575980) self.assertEqual(alignment.thickEnd, 53575997) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 61646095) self.assertEqual(alignment.thickEnd, 61646111) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) self.assertRaises(StopIteration, next, alignments) def test_reading_psl_34_004(self): """Test parsing psl_34_004.psl.bb.""" # The bigPsl file psl_34_004.psl.bb was generated using these commands: # pslToBigPsl -fa=fasta_34.fa psl_34_004.psl stdout | sort -k1,1 -k2,2n > psl_34_004.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as psl_34_004.bigPslInput hg19.chrom.sizes psl_34_004.psl.bb path = "Blat/psl_34_004.psl.bb" alignments = Align.parse(path, "bigpsl") self.check_psl_34_004(alignments) def test_writing_psl_34_004(self): """Test writing psl_34_004.psl.bb.""" path = "Blat/psl_34_004.psl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", fa=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_psl_34_004(alignments) def check_psl_34_004(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 10) self.assertEqual(alignments.targets[0].id, "chr1") self.assertEqual(len(alignments.targets[0]), 249250621) self.assertEqual(alignments.targets[1].id, "chr10") self.assertEqual(len(alignments.targets[1]), 135534747) self.assertEqual(alignments.targets[2].id, "chr13") self.assertEqual(len(alignments.targets[2]), 115169878) self.assertEqual(alignments.targets[3].id, "chr18") self.assertEqual(len(alignments.targets[3]), 78077248) self.assertEqual(alignments.targets[4].id, "chr19") self.assertEqual(len(alignments.targets[4]), 59128983) self.assertEqual(alignments.targets[5].id, "chr2") self.assertEqual(len(alignments.targets[5]), 243199373) self.assertEqual(alignments.targets[6].id, "chr22") self.assertEqual(len(alignments.targets[6]), 51304566) self.assertEqual(alignments.targets[7].id, "chr4") self.assertEqual(len(alignments.targets[7]), 191154276) self.assertEqual(alignments.targets[8].id, "chr8") self.assertEqual(len(alignments.targets[8]), 146364022) self.assertEqual(alignments.targets[9].id, "chr9") self.assertEqual(len(alignments.targets[9]), 141213431) self.assertEqual(len(alignments), 19) alignment = next(alignments) self.assertEqual(alignment.matches, 50) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 1207056) self.assertEqual(alignment.thickEnd, 1207106) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 39368490) self.assertEqual(alignment.thickEnd, 39368526) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 31) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 61700837) self.assertEqual(alignment.thickEnd, 61700871) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 220325687) self.assertEqual(alignment.thickEnd, 220325721) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 99388555) self.assertEqual(alignment.thickEnd, 99388591) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 24) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 112178171) self.assertEqual(alignment.thickEnd, 112178196) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 52759147) self.assertEqual(alignment.thickEnd, 52759198) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 54)) 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.assertEqual(len(alignment.target.seq), 115169878) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759160, 52759198], [ 1, 8, 8, 11, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 9: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 9: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 9) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 9) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 23891310) self.assertEqual(alignment.thickEnd, 23891349) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 27) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 43252217) self.assertEqual(alignment.thickEnd, 43252245) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.matches, 36) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 553742) self.assertEqual(alignment.thickEnd, 553781) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 34) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 35483340) self.assertEqual(alignment.thickEnd, 35483510) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 10, 35, 35, 46]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 54017130) self.assertEqual(alignment.thickEnd, 54017169) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 120641740) self.assertEqual(alignment.thickEnd, 120641776) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 43) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 183925984) self.assertEqual(alignment.thickEnd, 183926028) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 48)) 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183925990, 183926028], [ 1, 7, 11, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 4: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 4: internal_insertions = 4: open_internal_insertions = 1, extend_internal_insertions = 3; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 4) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 4) self.assertEqual(counts.insertions, 4) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 4) self.assertEqual(counts.aligned, 44) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 42144400) self.assertEqual(alignment.thickEnd, 42144436) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 48997405) self.assertEqual(alignment.thickEnd, 48997442) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) self.assertEqual(alignment.matches, 28) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 37558157) self.assertEqual(alignment.thickEnd, 37558191) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 44)) 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.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558173, 37558191], [ 49, 39, 39, 29, 11]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 16: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 16: internal_insertions = 10: open_internal_insertions = 1, extend_internal_insertions = 9; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 10) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 16) self.assertEqual(counts.insertions, 10) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 16) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.matches, 41) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 95160479) self.assertEqual(alignment.thickEnd, 95160520) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 146364022) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.matches, 38) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 85737865) self.assertEqual(alignment.thickEnd, 85737906) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 141213431) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) self.assertRaises(StopIteration, next, alignments) def test_reading_psl_34_005(self): """Test parsing psl_34_005.psl.bb.""" # The bigPsl file psl_34_005.psl.bb was generated using these commands: # pslToBigPsl -fa=fasta_34.fa psl_34_005.psl stdout | sort -k1,1 -k2,2n > psl_34_005.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as psl_34_005.bigPslInput hg19.chrom.sizes psl_34_005.psl.bb path = "Blat/psl_34_005.psl.bb" alignments = Align.parse(path, "bigpsl") self.check_psl_34_005(alignments) def test_writing_psl_34_005(self): """Test writing psl_34_005.psl.bb.""" path = "Blat/psl_34_005.psl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", fa=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_psl_34_005(alignments) def check_psl_34_005(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 10) self.assertEqual(alignments.targets[0].id, "chr1") self.assertEqual(len(alignments.targets[0]), 249250621) self.assertEqual(alignments.targets[1].id, "chr10") self.assertEqual(len(alignments.targets[1]), 135534747) self.assertEqual(alignments.targets[2].id, "chr13") self.assertEqual(len(alignments.targets[2]), 115169878) self.assertEqual(alignments.targets[3].id, "chr18") self.assertEqual(len(alignments.targets[3]), 78077248) self.assertEqual(alignments.targets[4].id, "chr19") self.assertEqual(len(alignments.targets[4]), 59128983) self.assertEqual(alignments.targets[5].id, "chr2") self.assertEqual(len(alignments.targets[5]), 243199373) self.assertEqual(alignments.targets[6].id, "chr22") self.assertEqual(len(alignments.targets[6]), 51304566) self.assertEqual(alignments.targets[7].id, "chr4") self.assertEqual(len(alignments.targets[7]), 191154276) self.assertEqual(alignments.targets[8].id, "chr8") self.assertEqual(len(alignments.targets[8]), 146364022) self.assertEqual(alignments.targets[9].id, "chr9") self.assertEqual(len(alignments.targets[9]), 141213431) self.assertEqual(len(alignments), 22) alignment = next(alignments) self.assertEqual(alignment.matches, 50) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 1207056) self.assertEqual(alignment.thickEnd, 1207106) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 10271783) self.assertEqual(alignment.thickEnd, 10271816) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 39368490) self.assertEqual(alignment.thickEnd, 39368526) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 31) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 61700837) self.assertEqual(alignment.thickEnd, 61700871) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 220325687) self.assertEqual(alignment.thickEnd, 220325721) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 99388555) self.assertEqual(alignment.thickEnd, 99388591) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 24) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 112178171) self.assertEqual(alignment.thickEnd, 112178196) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 52759147) self.assertEqual(alignment.thickEnd, 52759198) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 54)) 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.assertEqual(len(alignment.target.seq), 115169878) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759160, 52759198], [ 1, 8, 8, 11, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 9: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 9: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 9) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 9) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 23891310) self.assertEqual(alignment.thickEnd, 23891349) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 27) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 43252217) self.assertEqual(alignment.thickEnd, 43252245) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.matches, 36) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 553742) self.assertEqual(alignment.thickEnd, 553781) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 34) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 35483340) self.assertEqual(alignment.thickEnd, 35483510) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 10, 35, 35, 46]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 54017130) self.assertEqual(alignment.thickEnd, 54017169) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.matches, 17) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 53575980) self.assertEqual(alignment.thickEnd, 53575997) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 120641740) self.assertEqual(alignment.thickEnd, 120641776) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 43) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 183925984) self.assertEqual(alignment.thickEnd, 183926028) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 48)) 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.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183925990, 183926028], [ 1, 7, 11, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 4: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 4: internal_insertions = 4: open_internal_insertions = 1, extend_internal_insertions = 3; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 4) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 4) self.assertEqual(counts.insertions, 4) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 4) self.assertEqual(counts.aligned, 44) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 42144400) self.assertEqual(alignment.thickEnd, 42144436) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 48997405) self.assertEqual(alignment.thickEnd, 48997442) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) self.assertEqual(alignment.matches, 28) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 37558157) self.assertEqual(alignment.thickEnd, 37558191) self.assertEqual(alignment.itemRgb, "0") self.assertEqual(alignment.shape, (2, 44)) 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.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558173, 37558191], [ 49, 39, 39, 29, 11]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 16: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 16: internal_insertions = 10: open_internal_insertions = 1, extend_internal_insertions = 9; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 10) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 16) self.assertEqual(counts.insertions, 10) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 16) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 61646095) self.assertEqual(alignment.thickEnd, 61646111) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 33) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) self.assertEqual(alignment.matches, 41) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 95160479) self.assertEqual(alignment.thickEnd, 95160520) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 146364022) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.matches, 38) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 85737865) self.assertEqual(alignment.thickEnd, 85737906) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 141213431) self.assertEqual(len(alignment.query.seq), 50) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) self.assertRaises(StopIteration, next, alignments) class TestAlign_dnax_prot(unittest.TestCase): queries = { record.id: record.seq for record in SeqIO.parse("Blat/CAG33136.1.fasta", "fasta") } def test_reading_psl_35_001(self): """Test parsing psl_35_001.psl.bb.""" # The bigPsl file psl_35_001.psl.bb was generated using these commands: # pslToBigPsl -fa=CAG33136.1.fasta psl_35_001.psl stdout | sort -k1,1 -k2,2n > psl_35_001.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as psl_35_001.bigPslInput hg38.chrom.sizes psl_35_001.psl.bb path = "Blat/psl_35_001.psl.bb" alignments = Align.parse(path, "bigpsl") self.check_psl_35_001(alignments) def test_writing_psl_35_001(self): """Test writing psl_35_001.psl.bb.""" path = "Blat/psl_35_001.psl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", fa=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_psl_35_001(alignments) def check_psl_35_001(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 2) self.assertEqual(alignments.targets[0].id, "chr13") self.assertEqual(len(alignments.targets[0]), 114364328) self.assertEqual(alignments.targets[1].id, "chr4") self.assertEqual(len(alignments.targets[1]), 190214555) self.assertEqual(len(alignments), 8) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 75549820) self.assertEqual(alignment.thickEnd, 75567312) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75549820, 75549865, 75567225, 75567225, 75567312], [ 0, 15, 15, 113, 142]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 132: identities = 0, mismatches = 0. gaps = 17458: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 17458: internal_insertions = 98: open_internal_insertions = 1, extend_internal_insertions = 97; internal_deletions = 17360: open_internal_deletions = 1, extend_internal_deletions = 17359; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 98) self.assertEqual(counts.internal_deletions, 17360) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 17458) self.assertEqual(counts.insertions, 98) self.assertEqual(counts.deletions, 17360) self.assertEqual(counts.gaps, 17458) self.assertEqual(counts.aligned, 132) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 75560749) self.assertEqual(alignment.thickEnd, 75560881) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75560749, 75560881], [ 17, 61]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 132: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 132) alignment = next(alignments) self.assertEqual(alignment.matches, 52) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 75566694) self.assertEqual(alignment.thickEnd, 75566850) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75566694, 75566850], [ 61, 113]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 156: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 156) alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 75569459) self.assertEqual(alignment.thickEnd, 75569507) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75569459, 75569507], [ 142, 158]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 48: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 48) alignment = next(alignments) self.assertEqual(alignment.matches, 25) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 75594914) self.assertEqual(alignment.thickEnd, 75594989) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75594914, 75594989], [ 158, 183]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 75: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 75) alignment = next(alignments) self.assertEqual(alignment.matches, 47) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 75604767) self.assertEqual(alignment.thickEnd, 75605809) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75604767, 75604827, 75605728, 75605809], [ 183, 203, 203, 230]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 141: identities = 0, mismatches = 0. gaps = 901: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 901: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 901: open_internal_deletions = 1, extend_internal_deletions = 900; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 901) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 901) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 901) self.assertEqual(counts.gaps, 901) self.assertEqual(counts.aligned, 141) alignment = next(alignments) self.assertEqual(alignment.matches, 37) self.assertEqual(alignment.misMatches, 26) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 41257605) self.assertEqual(alignment.thickEnd, 41263290) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 190214555) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41257605, 41257731, 41263227, 41263227, 41263290], [ 17, 59, 59, 162, 183]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 189: identities = 0, mismatches = 0. gaps = 5599: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5599: internal_insertions = 103: open_internal_insertions = 1, extend_internal_insertions = 102; internal_deletions = 5496: open_internal_deletions = 1, extend_internal_deletions = 5495; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 103) self.assertEqual(counts.internal_deletions, 5496) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5599) self.assertEqual(counts.insertions, 103) self.assertEqual(counts.deletions, 5496) self.assertEqual(counts.gaps, 5599) self.assertEqual(counts.aligned, 189) alignment = next(alignments) self.assertEqual(alignment.matches, 26) self.assertEqual(alignment.misMatches, 8) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 41260685) self.assertEqual(alignment.thickEnd, 41260787) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 190214555) self.assertEqual(len(alignment.query.seq), 230) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41260685, 41260787], [ 76, 110]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 102: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 102) self.assertRaises(StopIteration, next, alignments) def check_psl_35_002(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 2) self.assertEqual(alignments.targets[0].id, "KI537194") self.assertEqual(len(alignments.targets[0]), 37111980) self.assertEqual(alignments.targets[1].id, "KI537979") self.assertEqual(len(alignments.targets[1]), 14052872) self.assertEqual(len(alignments), 2) alignment = next(alignments) self.assertEqual(alignment.matches, 204) self.assertEqual(alignment.misMatches, 6) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 20872390) self.assertEqual(alignment.thickEnd, 20873021) self.assertEqual(alignment.itemRgb, "0") self.assertGreater(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, "KI537194") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 37111980) self.assertEqual(len(alignment.query.seq), 230) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[20873021, 20872472, 20872471, 20872471, 20872390], [ 0, 183, 183, 203, 230]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 630: identities = 0, mismatches = 0. gaps = 21: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 21: internal_insertions = 20: open_internal_insertions = 1, extend_internal_insertions = 19; internal_deletions = 1: open_internal_deletions = 1, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 20) self.assertEqual(counts.internal_deletions, 1) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 21) self.assertEqual(counts.insertions, 20) self.assertEqual(counts.deletions, 1) self.assertEqual(counts.gaps, 21) self.assertEqual(counts.aligned, 630) alignment = next(alignments) self.assertEqual(alignment.matches, 210) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 9712654) self.assertEqual(alignment.thickEnd, 9744592) self.assertEqual(alignment.itemRgb, "0") 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.assertEqual(len(alignment.target.seq), 14052872) self.assertEqual(len(alignment.query.seq), 230) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[9712654, 9712786, 9715941, 9716097, 9716445, 9716532, 9718374, 9718422, 9739264, 9739339, 9743706, 9743766, 9744511, 9744592], [ 17, 61, 61, 113, 113, 142, 142, 158, 158, 183, 183, 203, 203, 230]]), # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 639: identities = 0, mismatches = 0. gaps = 31299: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 31299: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 31299: open_internal_deletions = 6, extend_internal_deletions = 31293; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 31299) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 31299) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 31299) self.assertEqual(counts.gaps, 31299) self.assertEqual(counts.aligned, 639) self.assertRaises(StopIteration, next, alignments) def test_reading_psl_35_002(self): """Test parsing psl_35_002.psl.bb.""" # The bigPsl file psl_35_002.psl.bb was generated using these commands: # pslToBigPsl -fa=CAG33136.1.fasta psl_35_002.psl stdout | grep -v KI538594 | sort -k1,1 -k2,2n > psl_35_002.bigPslInput # (where we excluded KI538594 because its alignment has a negative gap) # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as psl_35_002.bigPslInput balAcu1.chrom.sizes psl_35_002.psl.bb # See below for a description of the file balAcu1.fa. # We use this file here so we can check the SeqFeatures. records = SeqIO.parse("Blat/balAcu1.fa", "fasta") self.dna = {} for record in records: name, start_end = record.id.split(":") start, end = start_end.split("-") start = int(start) end = int(end) sequence = str(record.seq) self.dna[name] = Seq({start: sequence}, length=end) path = "Blat/psl_35_002.psl.bb" alignments = Align.parse(path, "bigpsl") self.check_psl_35_002(alignments) def test_writing_psl_35_002(self): """Test writing psl_35_002.psl.bb.""" path = "Blat/psl_35_002.psl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", fa=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_psl_35_002(alignments) class TestAlign_bigpsl(unittest.TestCase): # The bigPsl file bigPsl.bb was generated from the UCSC example files using these commands: # pslToBigPsl bigPsl.psl -cds=bigPsl.cds stdout | sort -k1,1 -k2,2n > bigPsl.txt # bedToBigBed -as=bigPsl.as -type=bed12+13 -tab bigPsl.txt hg38.chrom.sizes bigPsl.bb # (see https://genome.ucsc.edu/goldenPath/help/bigPsl.html) def test_reading(self): """Test parsing bigPsl.bb.""" path = "Blat/bigPsl.bb" alignments = Align.parse(path, "bigpsl") self.check_alignments(alignments) def test_writing(self): """Test writing bigPsl.bb.""" path = "Blat/bigPsl.bb" alignments = Align.parse(path, "bigpsl") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigpsl", cds=True) output.flush() output.seek(0) alignments = Align.parse(output, "bigpsl") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual(alignments.declaration, Align.bigpsl.declaration) self.assertEqual(len(alignments.targets), 1) self.assertEqual(alignments.targets[0].id, "chr1") self.assertEqual(len(alignments.targets[0]), 248956422) self.assertEqual(len(alignments), 100) alignment = next(alignments) self.assertEqual(alignment.matches, 1579) self.assertEqual(alignment.misMatches, 25) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.thickStart, 12622) self.assertEqual(alignment.thickEnd, 13259) self.assertEqual(alignment.itemRgb, "0") 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, "mAM992877") self.assertEqual(len(alignment.target.seq), 248956422) self.assertEqual(len(alignment.query.seq), 1604) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12612, 12721, 13220, 14361], [ 0, 354, 354, 463, 463, 1604]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1604: identities = 0, mismatches = 0. gaps = 884: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 884: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 884: open_internal_deletions = 2, extend_internal_deletions = 882; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 884) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 884) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 884) self.assertEqual(counts.gaps, 884) self.assertEqual(counts.aligned, 1604) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992881") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(382), ExactPosition(718), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12594, 12721, 13402, 14361], [0, 354, 354, 481, 481, 1440]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1440: identities = 0, mismatches = 0. gaps = 1048: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1048: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1048: open_internal_deletions = 2, extend_internal_deletions = 1046; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1048) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1048) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1048) self.assertEqual(counts.gaps, 1048) self.assertEqual(counts.aligned, 1440) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992878") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(733), ExactPosition(1003), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12645, 12697, 13220, 13656, 13658, 13957, 13958, 14362], [ 0, 354, 354, 406, 406, 842, 842, 1141, 1141, 1545]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1545: identities = 0, mismatches = 0. gaps = 944: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 944: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 944: open_internal_deletions = 4, extend_internal_deletions = 940; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 944) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 944) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 944) self.assertEqual(counts.gaps, 944) self.assertEqual(counts.aligned, 1545) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992879") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(364), ExactPosition(502), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12612, 12721, 13220, 14362], [ 0, 354, 354, 463, 463, 1605]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1605: identities = 0, mismatches = 0. gaps = 884: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 884: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 884: open_internal_deletions = 2, extend_internal_deletions = 882; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 884) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 884) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 884) self.assertEqual(counts.gaps, 884) self.assertEqual(counts.aligned, 1605) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992871") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(1401), ExactPosition(1632), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12612, 12721, 13220, 14409], [ 0, 354, 354, 463, 463, 1652]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1652: identities = 0, mismatches = 0. gaps = 884: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 884: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 884: open_internal_deletions = 2, extend_internal_deletions = 882; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 884) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 884) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 884) self.assertEqual(counts.gaps, 884) self.assertEqual(counts.aligned, 1652) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992872") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(1401), ExactPosition(1632), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12612, 12721, 13220, 14409], [ 0, 354, 354, 463, 463, 1652]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1652: identities = 0, mismatches = 0. gaps = 884: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 884: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 884: open_internal_deletions = 2, extend_internal_deletions = 882; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 884) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 884) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 884) self.assertEqual(counts.gaps, 884) self.assertEqual(counts.aligned, 1652) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992875") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(1401), ExactPosition(1632), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12612, 12721, 13220, 14409], [ 0, 354, 354, 463, 463, 1652]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1652: identities = 0, mismatches = 0. gaps = 884: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 884: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 884: open_internal_deletions = 2, extend_internal_deletions = 882; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 884) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 884) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 884) self.assertEqual(counts.gaps, 884) self.assertEqual(counts.aligned, 1652) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992880") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(316), ExactPosition(718), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12594, 12721, 13402, 14409], [ 0, 354, 354, 481, 481, 1488]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1488: identities = 0, mismatches = 0. gaps = 1048: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1048: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1048: open_internal_deletions = 2, extend_internal_deletions = 1046; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1048) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1048) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1048) self.assertEqual(counts.gaps, 1048) self.assertEqual(counts.aligned, 1488) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC032353") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11873, 12227, 12612, 12721, 13220, 13957, 13958, 14258, 14270, 14409], [ 0, 354, 354, 463, 463, 1200, 1200, 1500, 1500, 1639]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1639: identities = 0, mismatches = 0. gaps = 897: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 897: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 897: open_internal_deletions = 4, extend_internal_deletions = 893; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 897) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 897) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 897) self.assertEqual(counts.gaps, 897) self.assertEqual(counts.aligned, 1639) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAM992873") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(BeforePosition(436), ExactPosition(706), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[12612, 12721, 13220, 13656, 13658, 13957, 13958, 14362], [ 0, 109, 109, 545, 545, 844, 844, 1248]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1248: identities = 0, mismatches = 0. gaps = 502: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 502: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 502: open_internal_deletions = 3, extend_internal_deletions = 499; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 502) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 502) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 502) self.assertEqual(counts.gaps, 502) self.assertEqual(counts.aligned, 1248) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD190877") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[12993, 13016], [0, 23]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 23: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 23) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD167845") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13001, 13024], [0, 23]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 23: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 23) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD469098") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13003, 13024], [2, 23]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 21: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 21) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD485136") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13087, 13107], [0, 20]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 20: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 20) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC070227") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[13420, 13957, 13958, 14259, 14271, 14407], [ 0, 537, 537, 838, 838, 974]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 974: identities = 0, mismatches = 0. gaps = 13: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 13: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 13: open_internal_deletions = 2, extend_internal_deletions = 11; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 13) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 13) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 13) self.assertEqual(counts.gaps, 13) self.assertEqual(counts.aligned, 974) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD282506") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13721, 13745], [0, 24]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 24: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 24) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD192765") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13877, 13909], [0, 32]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD191631") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13932, 13964], [0, 32]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD135207") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[13939, 13971], [0, 32]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD157229") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14002, 14023], [0, 21]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 21: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 21) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD199172") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14241, 14265], [0, 24]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 24: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 24) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD422311") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14246, 14278], [0, 32]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD108953") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14322, 14354], [0, 32]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD227419") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14378, 14407], [1, 30]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 29: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 29) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC063555") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14404, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16765, 16857, 17055, 17232, 17742, 17914, 18061, 18267, 18369, 18500, 18554, 18912, 19236], [ 2146, 2095, 2090, 1716, 1716, 1647, 1647, 1537, 1537, 1535, 1494, 1494, 1335, 1335, 1137, 1137, 627, 627, 480, 480, 378, 378, 324, 324, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2139: identities = 0, mismatches = 0. gaps = 2700: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2700: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 2693: open_internal_deletions = 10, extend_internal_deletions = 2683; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 2693) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 2700) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 2693) self.assertEqual(counts.gaps, 2700) self.assertEqual(counts.aligned, 2139) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC063893") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14404, 14511, 14513, 14829, 14969, 15038, 15795, 15903, 15903, 15947, 16606, 16765, 16857, 17055, 17232, 17358, 17361, 17742, 17914, 18061, 18267, 18366, 18912, 19720], [ 2563, 2456, 2456, 2140, 2140, 2071, 2071, 1963, 1962, 1918, 1918, 1759, 1759, 1561, 1561, 1435, 1435, 1054, 1054, 907, 907, 808, 808, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2562: identities = 0, mismatches = 0. gaps = 2755: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2755: internal_insertions = 1: open_internal_insertions = 1, extend_internal_insertions = 0; internal_deletions = 2754: open_internal_deletions = 10, extend_internal_deletions = 2744; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 1) self.assertEqual(counts.internal_deletions, 2754) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 2755) self.assertEqual(counts.insertions, 1) self.assertEqual(counts.deletions, 2754) self.assertEqual(counts.gaps, 2755) self.assertEqual(counts.aligned, 2562) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC053987") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14404, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16765, 16857, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18366, 18912, 19763], [ 2379, 2328, 2323, 1949, 1949, 1880, 1880, 1770, 1770, 1768, 1727, 1727, 1568, 1568, 1370, 1370, 1234, 1234, 1097, 1097, 950, 950, 851, 851, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2372: identities = 0, mismatches = 0. gaps = 2994: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2994: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 2987: open_internal_deletions = 10, extend_internal_deletions = 2977; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 2987) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 2994) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 2987) self.assertEqual(counts.gaps, 2994) self.assertEqual(counts.aligned, 2372) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAL137714") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( CompoundLocation( [ SimpleLocation( ExactPosition(168), ExactPosition(318), strand=1 ), SimpleLocation( ExactPosition(311), ExactPosition(704), strand=1 ), SimpleLocation( ExactPosition(940), ExactPosition(1273), strand=1 ), SimpleLocation( ExactPosition(3005), ExactPosition(3209), strand=1 ), ], "join", ), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 14404, 14511, 14513, 14829, 14969, 15250, 185765, 186064, 186064, 186623, 186626, 187287, 187379, 187577, 187754, 188266, 188438, 188485, 188485, 188584, 188790, 188889, 195262, 195416, 199836, 199999], [ 3498, 3391, 3391, 3075, 3075, 2794, 2794, 2495, 2493, 1934, 1934, 1273, 1273, 1075, 1075, 563, 563, 516, 515, 416, 416, 317, 317, 163, 163, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 3495: identities = 0, mismatches = 0. gaps = 182103: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 182103: internal_insertions = 3: open_internal_insertions = 2, extend_internal_insertions = 1; internal_deletions = 182100: open_internal_deletions = 10, extend_internal_deletions = 182090; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 182100) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 182103) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 182100) self.assertEqual(counts.gaps, 182103) self.assertEqual(counts.aligned, 3495) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC048328") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14404, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16722, 16722, 16768, 16856, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18379, 24737, 24891], [ 1720, 1669, 1664, 1290, 1290, 1221, 1221, 1111, 1111, 1109, 1068, 1068, 952, 943, 897, 897, 698, 698, 562, 562, 425, 425, 278, 278, 166, 166, 12]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1692: identities = 0, mismatches = 0. gaps = 8811: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 8811: internal_insertions = 16: open_internal_insertions = 3, extend_internal_insertions = 13; internal_deletions = 8795: open_internal_deletions = 10, extend_internal_deletions = 8785; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 16) self.assertEqual(counts.internal_deletions, 8795) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 8811) self.assertEqual(counts.insertions, 16) self.assertEqual(counts.deletions, 8795) self.assertEqual(counts.gaps, 8811) self.assertEqual(counts.aligned, 1692) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC063470") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14404, 14455, 14455, 14829, 15795, 15905, 15906, 15906, 15947, 16606, 16765, 16857, 17055, 17605, 18061, 24737, 24891, 29320, 29346], [ 1576, 1525, 1520, 1146, 1146, 1036, 1036, 1034, 993, 993, 834, 834, 636, 636, 180, 180, 26, 26, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1569: identities = 0, mismatches = 0. gaps = 13380: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 13380: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 13373: open_internal_deletions = 7, extend_internal_deletions = 13366; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 13373) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 13380) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 13373) self.assertEqual(counts.gaps, 13380) self.assertEqual(counts.aligned, 1569) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBX537637") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( CompoundLocation( [ SimpleLocation( ExactPosition(240), ExactPosition(432), strand=1 ), SimpleLocation( ExactPosition(431), ExactPosition(1166), strand=1 ), SimpleLocation( ExactPosition(1165), ExactPosition(1591), strand=1 ), ], "join", ), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14404, 14495, 14559, 14571, 15004, 15038, 15795, 15903, 15903, 15947, 16606, 16765, 16857, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18366, 24737, 24891, 29533, 29809], [ 1597, 1506, 1506, 1494, 1494, 1460, 1460, 1352, 1351, 1307, 1307, 1148, 1148, 950, 950, 814, 814, 677, 677, 530, 530, 431, 431, 277, 277, 1]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1595: identities = 0, mismatches = 0. gaps = 13811: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 13811: internal_insertions = 1: open_internal_insertions = 1, extend_internal_insertions = 0; internal_deletions = 13810: open_internal_deletions = 11, extend_internal_deletions = 13799; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 1) self.assertEqual(counts.internal_deletions, 13810) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 13811) self.assertEqual(counts.insertions, 1) self.assertEqual(counts.deletions, 13810) self.assertEqual(counts.gaps, 13811) self.assertEqual(counts.aligned, 1595) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAK024481") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(BeforePosition(1345), ExactPosition(1897), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14406, 15905, 15906, 15906, 16765, 16857, 18733], [ 4236, 2737, 2737, 2735, 1876, 1876, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 4234: identities = 0, mismatches = 0. gaps = 95: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 95: internal_insertions = 2: open_internal_insertions = 1, extend_internal_insertions = 1; internal_deletions = 93: open_internal_deletions = 2, extend_internal_deletions = 91; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 2) self.assertEqual(counts.internal_deletions, 93) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 95) self.assertEqual(counts.insertions, 2) self.assertEqual(counts.deletions, 93) self.assertEqual(counts.gaps, 95) self.assertEqual(counts.aligned, 4234) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAK057951") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 14406, 14829, 14969, 15038, 15795, 15903, 15903, 15947, 16606, 16768, 16856, 17055, 17232, 17368, 17605, 17745, 18036, 18061, 18267, 18366, 24737, 24893, 188471, 188485, 188485, 188584, 188790, 188889, 195262, 195416, 199836, 199861], [ 1954, 1531, 1531, 1462, 1462, 1354, 1353, 1309, 1309, 1147, 1147, 948, 948, 812, 812, 672, 672, 647, 647, 548, 548, 392, 392, 378, 377, 278, 278, 179, 179, 25, 25, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1952: identities = 0, mismatches = 0. gaps = 183505: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 183505: internal_insertions = 2: open_internal_insertions = 2, extend_internal_insertions = 0; internal_deletions = 183503: open_internal_deletions = 13, extend_internal_deletions = 183490; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 2) self.assertEqual(counts.internal_deletions, 183503) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 183505) self.assertEqual(counts.insertions, 2) self.assertEqual(counts.deletions, 183503) self.assertEqual(counts.gaps, 183505) self.assertEqual(counts.aligned, 1952) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAK092583") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(72), ExactPosition(555), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14406, 14455, 14455, 15905, 15906, 15906, 16765, 16857, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 24737, 24891, 29320, 29344], [ 3161, 3112, 3107, 1657, 1657, 1655, 796, 796, 598, 598, 462, 462, 325, 325, 178, 178, 24, 24, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 3154: identities = 0, mismatches = 0. gaps = 11791: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 11791: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 11784: open_internal_deletions = 7, extend_internal_deletions = 11777; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 11784) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 11791) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 11784) self.assertEqual(counts.gaps, 11791) self.assertEqual(counts.aligned, 3154) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAX747611") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14406, 14455, 14455, 15905, 15906, 15906, 16765, 16857, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 24737, 24891, 29320, 29344], [ 3161, 3112, 3107, 1657, 1657, 1655, 796, 796, 598, 598, 462, 462, 325, 325, 178, 178, 24, 24, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 3154: identities = 0, mismatches = 0. gaps = 11791: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 11791: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 11784: open_internal_deletions = 7, extend_internal_deletions = 11777; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 11784) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 11791) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 11784) self.assertEqual(counts.gaps, 11791) self.assertEqual(counts.aligned, 3154) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAK056232") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14406, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16768, 16856, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18366, 24737, 24891, 29320, 29902, 29912, 30000], [ 2354, 2305, 2300, 1926, 1926, 1857, 1857, 1747, 1747, 1745, 1704, 1704, 1542, 1542, 1343, 1343, 1207, 1207, 1070, 1070, 923, 923, 824, 824, 670, 670, 88, 88, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2347: identities = 0, mismatches = 0. gaps = 13254: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 13254: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 13247: open_internal_deletions = 12, extend_internal_deletions = 13235; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 13247) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 13254) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 13247) self.assertEqual(counts.gaps, 13254) self.assertEqual(counts.aligned, 2347) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC094698") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14407, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16765, 16857, 17055, 17232, 17742, 17914, 18061, 18267, 19108], [ 2504, 2456, 2451, 2077, 2077, 2008, 2008, 1898, 1898, 1896, 1855, 1855, 1696, 1696, 1498, 1498, 988, 988, 841, 841, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2497: identities = 0, mismatches = 0. gaps = 2211: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2211: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 2204: open_internal_deletions = 8, extend_internal_deletions = 2196; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 2204) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 2211) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 2204) self.assertEqual(counts.gaps, 2211) self.assertEqual(counts.aligned, 2497) alignment = next(alignments) self.assertEqual(alignment.query.id, "mBC041177") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14407, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16722, 16731, 16768, 16856, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18379, 18912, 19190, 19191, 19716], [ 2336, 2288, 2283, 1909, 1909, 1840, 1840, 1730, 1730, 1728, 1687, 1687, 1571, 1571, 1534, 1534, 1335, 1335, 1199, 1199, 1062, 1062, 915, 915, 803, 803, 525, 525, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2329: identities = 0, mismatches = 0. gaps = 2987: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2987: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 2980: open_internal_deletions = 12, extend_internal_deletions = 2968; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 2980) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 2987) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 2980) self.assertEqual(counts.gaps, 2987) self.assertEqual(counts.aligned, 2329) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAY217347") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(1303), ExactPosition(2089), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14407, 14455, 14455, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16722, 16731, 16768, 16856, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18379, 18912, 19759], [ 2382, 2334, 2329, 1955, 1955, 1886, 1886, 1776, 1776, 1774, 1733, 1733, 1617, 1617, 1580, 1580, 1381, 1381, 1245, 1245, 1108, 1108, 961, 961, 849, 849, 2]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 2373: identities = 0, mismatches = 0. gaps = 2986: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2986: internal_insertions = 7: open_internal_insertions = 2, extend_internal_insertions = 5; internal_deletions = 2979: open_internal_deletions = 11, extend_internal_deletions = 2968; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 7) self.assertEqual(counts.internal_deletions, 2979) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 2986) self.assertEqual(counts.insertions, 7) self.assertEqual(counts.deletions, 2979) self.assertEqual(counts.gaps, 2986) self.assertEqual(counts.aligned, 2373) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD043865") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14423, 14455], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD464022") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14453, 14485], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD464023") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14455, 14485], [30, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 30: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 30) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD426250") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14496, 14528], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD319762") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14537, 14569], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD439184") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14538, 14570], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAK289708") self.assertEqual(len(alignment.query.features), 1) self.assertEqual( alignment.query.features[0], SeqFeature( SimpleLocation(ExactPosition(146), ExactPosition(1553), strand=1), type="CDS", ), ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[14570, 14829, 14969, 15038, 15795, 15905, 15906, 15906, 15947, 16606, 16722, 16722, 16768, 16856, 17055, 17232, 17368, 17605, 17742, 17914, 18061, 18267, 18379, 24737, 24891, 29823, 29961], [ 1678, 1419, 1419, 1350, 1350, 1240, 1240, 1238, 1197, 1197, 1081, 1072, 1026, 1026, 827, 827, 691, 691, 554, 554, 407, 407, 295, 295, 141, 141, 3]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1664: identities = 0, mismatches = 0. gaps = 13738: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 13738: internal_insertions = 11: open_internal_insertions = 2, extend_internal_insertions = 9; internal_deletions = 13727: open_internal_deletions = 11, extend_internal_deletions = 13716; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 11) self.assertEqual(counts.internal_deletions, 13727) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 13738) self.assertEqual(counts.insertions, 11) self.assertEqual(counts.deletions, 13727) self.assertEqual(counts.gaps, 13738) self.assertEqual(counts.aligned, 1664) alignment = next(alignments) self.assertEqual(alignment.query.id, "mDQ588205") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14629, 14657], [0, 28]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD033185") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14643, 14667], [0, 24]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 24: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 24) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD386972") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14643, 14667], [24, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 24: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 24) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD469492") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14673, 14705], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD371043") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[14702, 14717, 14720, 14737], [32, 17, 17, 0]]), ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 3: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 3: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 3: open_internal_deletions = 1, extend_internal_deletions = 2; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 3) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 3) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 3) self.assertEqual(counts.gaps, 3) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD186991") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[14703, 14717, 14720, 14738], [32, 18, 18, 0]]), ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 3: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 3: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 3: open_internal_deletions = 1, extend_internal_deletions = 2; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 3) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 3) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 3) self.assertEqual(counts.gaps, 3) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD178321") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14704, 14725], [21, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 21: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 21) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD371044") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14705, 14737], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD492409") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14739, 14771], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD248147") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14746, 14770], [24, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 24: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 24) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD044295") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14785, 14817], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD433165") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14810, 14842], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD055458") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14823, 14855], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD131561") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14828, 14853], [25, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD129847") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14936, 14956], [20, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 20: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 20) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD219312") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[14950, 14971], [21, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 21: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 21) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD546847") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15086, 15118], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD218460") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15097, 15129], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mKJ806766") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[15118, 15122, 15122, 15654], [9, 13, 14, 546]]), ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 536: identities = 0, mismatches = 0. gaps = 1: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1: internal_insertions = 1: open_internal_insertions = 1, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 1) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1) self.assertEqual(counts.insertions, 1) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 1) self.assertEqual(counts.aligned, 536) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD131237") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15187, 15219], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD128091") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15209, 15241], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD422546") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15274, 15305], [31, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 31: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 31) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD153435") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15292, 15324], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD367640") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15461, 15493], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD487131") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15468, 15500], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD493181") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15480, 15512], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD205712") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15558, 15590], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD425846") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15584, 15616], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD219639") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15603, 15634], [32, 1]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 31: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 31) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD078677") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15603, 15635], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD078676") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15614, 15635], [21, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 21: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 21) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD253503") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15643, 15675], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD253504") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15644, 15675], [31, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 31: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 31) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD159284") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15664, 15687], [23, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 23: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 23) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD115871") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15675, 15707], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD456634") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15677, 15709], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD487879") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15741, 15772], [32, 1]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 31: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 31) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD080014") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15741, 15773], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD336830") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15760, 15792], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD444008") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15761, 15793], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD460507") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15812, 15836], [24, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 24: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 24) alignment = next(alignments) self.assertEqual(alignment.query.id, "mAK308574") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[15870, 15903, 15903, 16027, 16606, 16765, 16857, 17055, 17232, 17364, 17521, 17742, 17914, 18061, 18267, 18366, 29320, 29359], [ 1153, 1120, 1119, 995, 995, 836, 836, 638, 638, 506, 506, 285, 285, 138, 138, 39, 39, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1152: identities = 0, mismatches = 0. gaps = 12338: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 12338: internal_insertions = 1: open_internal_insertions = 1, extend_internal_insertions = 0; internal_deletions = 12337: open_internal_deletions = 7, extend_internal_deletions = 12330; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 1) self.assertEqual(counts.internal_deletions, 12337) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 12338) self.assertEqual(counts.insertions, 1) self.assertEqual(counts.deletions, 12337) self.assertEqual(counts.gaps, 12338) self.assertEqual(counts.aligned, 1152) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD389037") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15906, 15936], [30, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 30: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 30) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD521711") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15947, 15979], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD383617") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15972, 16004], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD491045") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15982, 16014], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD318660") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[15985, 16017], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD341280") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16118, 16150], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD220623") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16157, 16189], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD465423") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16165, 16197], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD515432") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16176, 16208], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD542452") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16184, 16216], [32, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 32: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 32) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD507246") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16201, 16230], [30, 1]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 29: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 29) alignment = next(alignments) self.assertEqual(alignment.query.id, "mJD102852") self.assertEqual(len(alignment.query.features), 0) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[16253, 16274], [21, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 21: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 21) self.assertRaises(StopIteration, next, alignments) class TestAlign_searching(unittest.TestCase): # The BED file bigbedtest.bed contains the following data: # chr1 10 100 name1 1 + # chr1 29 39 name2 2 - # chr1 200 300 name3 3 + # chr2 50 50 name4 6 + # chr2 100 110 name5 4 + # chr2 200 210 name6 5 + # chr2 220 220 name7 6 + # chr3 0 0 name8 7 - # with chromosome sizes in bigbedtest.chrom.sizes: # chr1 1000 # chr2 2000 # chr3 1000 # The bigPsl file bigbedtest.psl.bb was generated using these commands: # bedToPsl bigbedtest.chrom.sizes bigbedtest.bed bigbedtest.psl # pslToBigPsl bigbedtest.psl stdout | sort -k1,1 -k2,2n > bigbedtest.bigPslInput # bedToBigBed -type=bed12+13 -tab -as=bigPsl.as bigbedtest.bigPslInput bigbedtest.chrom.sizes bigbedtest.psl.bb def test_search_chromosome(self): path = "Blat/bigbedtest.psl.bb" alignments = Align.parse(path, "bigpsl") self.assertEqual(alignments.declaration, Align.bigpsl.declaration) selected_alignments = alignments.search("chr2") names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name4", "name5", "name6", "name7"]) def test_search_region(self): path = "Blat/bigbedtest.psl.bb" alignments = Align.parse(path, "bigpsl") selected_alignments = alignments.search("chr2", 105, 1000) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name5", "name6", "name7"]) selected_alignments = alignments.search("chr2", 110, 1000) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name6", "name7"]) selected_alignments = alignments.search("chr2", 40, 50) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name4"]) selected_alignments = alignments.search("chr2", 50, 50) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name4"]) selected_alignments = alignments.search("chr2", 50, 200) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name4", "name5"]) selected_alignments = alignments.search("chr2", 200, 220) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name6", "name7"]) selected_alignments = alignments.search("chr2", 220, 220) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name7"]) def test_search_position(self): path = "Blat/bigbedtest.psl.bb" alignments = Align.parse(path, "bigpsl") selected_alignments = alignments.search("chr1", 250) names = [alignment.query.id for alignment in selected_alignments] self.assertEqual(names, ["name3"]) def test_three_iterators(self): """Create three iterators and use them concurrently.""" path = "Blat/bigbedtest.psl.bb" alignments1 = Align.parse(path, "bigpsl") alignments2 = alignments1.search("chr2") alignments3 = alignments1.search("chr2", 110, 1000) alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name1") alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name2") alignment2 = next(alignments2) self.assertEqual(alignment2.query.id, "name4") alignment2 = next(alignments2) self.assertEqual(alignment2.query.id, "name5") alignment2 = next(alignments2) self.assertEqual(alignment2.query.id, "name6") alignment3 = next(alignments3) self.assertEqual(alignment3.query.id, "name6") alignment3 = next(alignments3) self.assertEqual(alignment3.query.id, "name7") alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name3") alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name4") alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name5") alignment2 = next(alignments2) self.assertEqual(alignment2.query.id, "name7") self.assertRaises(StopIteration, next, alignments2) alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name6") alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name7") self.assertRaises(StopIteration, next, alignments3) alignment1 = next(alignments1) self.assertEqual(alignment1.query.id, "name8") self.assertRaises(StopIteration, next, alignments1) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)