# 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.bigbed module.""" import os import sys import tempfile import unittest from io import StringIO from Bio import Align from Bio import SeqIO from Bio.Align import bigbed from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.bigbed." ) from None for i, argument in enumerate(sys.argv): if argument == "--big": big = True sys.argv.pop(i) break else: big = False class TestAlign_dna_rna(unittest.TestCase): # The bigBed file dna_rna.bb was generated using the commands # sort -k1,1 -k2,2n dna_rna.bed > dna_rna.sorted.bed # twoBitInfo hg38.2bit hg38.chrom.sizes # bedToBigBed dna_rna.sorted.bed hg38.chrom.sizes dna_rna.bb path = "Blat/dna_rna.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 = Seq(data, length=198295559) # hg38 chr3 records = SeqIO.parse("Blat/rna.fa", "fasta") self.rna = {record.id: record.seq for record in records} def test_reading(self): """Test parsing dna_rna.bb.""" path = "Blat/dna_rna.bb" alignments = Align.parse(path, "bigbed") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(path, "bigbed") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "bigbed") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def test_writing(self): """Test writing dna_rna.bb.""" alignments = Align.parse(self.path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed") output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, ) 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.score, 1000) self.assertEqual(alignment.shape, (2, 1711)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606], [ 181, 118, 118, 43, 43, 0]]) # fmt: on ) ) alignment.target.seq = self.dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( 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") # The modified RNAs have gaps in their sequence. As this information is # not stored in a BED file, we cannot calculate the substitution matrix. 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.score, 978) self.assertEqual(alignment.shape, (2, 1711)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1_modified") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530922, 42530958, 42532020, 42532037, 42532039, 42532095, 42532563, 42532606], [ 179, 152, 116, 116, 99, 99, 43, 43, 0]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 179: identities = 0, mismatches = 0. gaps = 1532: 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 = 1532: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 1532) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1532) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1532) self.assertEqual(counts.gaps, 1532) self.assertEqual(counts.aligned, 179) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 5407)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_111921.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48663767, 48663813, 48665640, 48665722, 48669098, 48669174], [ 0, 46, 46, 128, 128, 204]]) # fmt: on ) ) alignment.target.seq = self.dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( 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") 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.score, 972) self.assertEqual(alignment.shape, (2, 5407)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_111921.1_modified") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48663767, 48663795, 48663796, 48663813, 48665640, 48665716, 48665722, 48669098, 48669174], [ 0, 28, 28, 45, 45, 121, 127, 127, 203]]) # fmt: on ) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 203: identities = 0, mismatches = 0. gaps = 5204: 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 = 5204: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 5204) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5204) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5204) self.assertEqual(counts.gaps, 5204) self.assertEqual(counts.aligned, 203) self.assertRaises(StopIteration, next, alignments) class TestAlign_dna(unittest.TestCase): # The bigBed file psl_34_001.bb was generated using the commands # sort -k1,1 -k2,2n psl_34_001.bed > psl_34_001.sorted.bed # twoBitInfo hg19.2bit hg19.chrom.sizes # bedToBigBed psl_34_001.sorted.bed hg19.chrom.sizes psl_34_001.bb # The bigBed file psl_34_003.bb was generated using the commands # sort -k1,1 -k2,2n psl_34_003.bed > psl_34_003.sorted.bed # twoBitInfo hg19.2bit hg19.chrom.sizes # bedToBigBed psl_34_003.sorted.bed hg19.chrom.sizes psl_34_003.bb # The bigBed file psl_34_004.bb was generated using the commands # sort -k1,1 -k2,2n psl_34_004.bed > psl_34_004.sorted.bed # twoBitInfo hg19.2bit hg19.chrom.sizes # bedToBigBed psl_34_004.sorted.bed hg19.chrom.sizes psl_34_004.bb # The bigBed file psl_34_005.bb was generated using the commands # sort -k1,1 -k2,2n psl_34_005.bed > psl_34_005.sorted.bed # twoBitInfo hg19.2bit hg19.chrom.sizes # bedToBigBed psl_34_005.sorted.bed hg19.chrom.sizes psl_34_005.bb def check_alignments_psl_34_001(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, ) 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.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( 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.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( 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.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 36, 0]]), # 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.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 0, 34]]), # 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.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 34, 0]]), # 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.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 36, 0]]), # 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.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 25, 0]]), # 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.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # 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 = 6: 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 = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 0, 39]]), # 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.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 0, 28]]), # 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.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 39, 0]]), # 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.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 39, 0]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 17, 0]]), # 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.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 36, 0]]), # 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.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # 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 = 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, 44) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 0, 36]]), # 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.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 37, 0]]), # 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.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # 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 = 6: 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 = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 0, 16]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 0, 41]]), # 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.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 0, 41]]), # 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_001(self): """Test reading psl_34_001.bb.""" path = "Blat/psl_34_001.bb" alignments = Align.parse(path, "bigbed") self.check_alignments_psl_34_001(alignments) def test_writing_psl_34_001(self): """Test writing psl_34_001.bb.""" path = "Blat/psl_34_001.bb" alignments = Align.parse(path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed") output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments_psl_34_001(alignments) def check_alignments_psl_34_003(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, ) 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.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( 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.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 17, 0]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 0, 16]]), # 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_003(self): """Test reading psl_34_003.bb.""" path = "Blat/psl_34_003.bb" alignments = Align.parse(path, "bigbed") self.check_alignments_psl_34_003(alignments) def test_writing_psl_34_003(self): """Test writing psl_34_003.bb.""" path = "Blat/psl_34_003.bb" alignments = Align.parse(path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed") output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments_psl_34_003(alignments) def check_alignments_psl_34_004(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, ) 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.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( 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.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 36, 0]]), # 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.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 0, 34]]), # 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.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 34, 0]]), # 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.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 36, 0]]), # 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.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 25, 0]]), # 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.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # 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 = 6: 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 = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 0, 39]]), # 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.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 0, 28]]), # 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.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 39, 0]]), # 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.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 39, 0]]), # 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.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 36, 0]]), # 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.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # 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 = 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, 44) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 0, 36]]), # 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.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 37, 0]]), # 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.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # 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 = 6: 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 = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 0, 41]]), # 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.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 0, 41]]), # 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_004(self): """Test reading psl_34_004.bb.""" path = "Blat/psl_34_004.bb" alignments = Align.parse(path, "bigbed") self.check_alignments_psl_34_004(alignments) def test_writing_psl_34_004(self): """Test writing psl_34_004.bb.""" path = "Blat/psl_34_004.bb" alignments = Align.parse(path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed") output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments_psl_34_004(alignments) def check_alignments_psl_34_005(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, ) 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.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( 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.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( 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.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 36, 0]]), # 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.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 0, 34]]), # 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.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 34, 0]]), # 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.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 36, 0]]), # 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.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 25, 0]]), # 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.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # 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 = 6: 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 = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 0, 39]]), # 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.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 0, 28]]), # 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.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 39, 0]]), # 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.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 39, 0]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 17, 0]]), # 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.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 36, 0]]), # 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.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # 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 = 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, 44) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 0, 36]]), # 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.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 37, 0]]), # 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.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # 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 = 6: 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 = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg18_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 0, 16]]), # 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.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 0, 41]]), # 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.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 0, 41]]), # 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 reading psl_34_005.bb.""" path = "Blat/psl_34_005.bb" alignments = Align.parse(path, "bigbed") self.check_alignments_psl_34_005(alignments) def test_writing_psl_34_005(self): """Test writing psl_34_005.bb.""" path = "Blat/psl_34_005.bb" alignments = Align.parse(path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed") output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments_psl_34_005(alignments) class TestAlign_dnax_prot(unittest.TestCase): # The bigBed file psl_35_001.bb was generated using the commands # sort -k1,1 -k2,2n psl_35_001.bed > psl_35_001.sorted.bed # twoBitInfo hg38.2bit hg38.chrom.sizes # bedToBigBed psl_35_001.sorted.bed hg38.chrom.sizes psl_35_001.bb path = "Blat/psl_35_001.bb" def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, ) 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.score, 986) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75549820, 75549865, 75567225, 75567312], [ 0, 45, 45, 132]]), # 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 = 17360: 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 = 17360: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 17360) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 17360) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 17360) self.assertEqual(counts.gaps, 17360) self.assertEqual(counts.aligned, 132) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75560749, 75560881], [ 0, 132]]), # 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.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75566694, 75566850], [ 0, 156]]), # 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.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75569459, 75569507], [ 0, 48]]), # 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.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75594914, 75594989], [ 0, 75]]), # 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.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75604767, 75604827, 75605728, 75605809], [ 0, 60, 60, 141]]), # 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.score, 166) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41257605, 41257731, 41263227, 41263290], [ 0, 126, 126, 189]]), # 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 = 5496: 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 = 5496: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; 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, 0) self.assertEqual(counts.internal_deletions, 5496) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5496) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5496) self.assertEqual(counts.gaps, 5496) self.assertEqual(counts.aligned, 189) alignment = next(alignments) self.assertEqual(alignment.score, 530) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41260685, 41260787], [ 0, 102]]), # 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 test_reading_psl_35_001(self): """Test parsing psl_35_001.bb.""" alignments = Align.parse(self.path, "bigbed") self.check_alignments(alignments) def test_writing_psl_35_001(self): """Test writing psl_35_001.bb.""" alignments = Align.parse(self.path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed") output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments(alignments) class TestAlign_bed12(unittest.TestCase): # The bigBed files were generated using the commands # twoBitInfo hg19.2bit hg19.chrom.sizes # bedToBigBed bed3.bed hg19.chrom.sizes bed3.bb # bedToBigBed bed4.bed hg19.chrom.sizes bed4.bb # bedToBigBed bed5.bed hg19.chrom.sizes bed5.bb # bedToBigBed bed6.bed hg19.chrom.sizes bed6.bb # bedToBigBed bed7.bed hg19.chrom.sizes bed7.bb # bedToBigBed bed8.bed hg19.chrom.sizes bed8.bb # bedToBigBed bed9.bed hg19.chrom.sizes bed9.bb # bedToBigBed bed12.bed hg19.chrom.sizes bed12.bb def check_autosql(self, declaration, bedN, msg): if bedN == 3: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" ) """, msg=msg, ) elif bedN == 4: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." ) """, msg=msg, ) elif bedN == 5: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" ) """, msg=msg, ) elif bedN == 6: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" ) """, msg=msg, ) elif bedN == 7: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" ) """, msg=msg, ) elif bedN == 8: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" ) """, msg=msg, ) elif bedN == 9: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" ) """, msg=msg, ) elif bedN == 12: self.assertEqual( str(declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) """, msg=msg, ) def check_alignments(self, alignments, bedN, msg): self.assertEqual(len(alignments), 2) alignment = next(alignments) if bedN >= 5: self.assertEqual(alignment.score, 960, msg=msg) self.assertEqual(alignment.shape, (2, 4000), msg=msg) self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=msg ) self.assertLess( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=msg ) self.assertEqual(len(alignment), 2, msg=msg) self.assertIs(alignment.sequences[0], alignment.target, msg=msg) self.assertIs(alignment.sequences[1], alignment.query, msg=msg) self.assertEqual(alignment.target.id, "chr22", msg=msg) if bedN >= 4: self.assertEqual(alignment.query.id, "mRNA1", msg=msg) else: self.assertIsNone(alignment.query.id, msg=msg) if bedN == 12: self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1000, 1567, 4512, 5000], [ 0, 567, 567, 1055]]), # fmt: on ), msg=msg, ) else: self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1000, 5000], [0, 4000]]), ), msg=msg, ) if bedN >= 7: self.assertEqual(alignment.thickStart, 1200, msg=msg) if bedN >= 8: self.assertEqual(alignment.thickEnd, 4900, msg=msg) if bedN >= 9: self.assertEqual(alignment.itemRgb, "255,0,0", msg=msg) alignment = next(alignments) if bedN >= 5: self.assertEqual(alignment.score, 900, msg=msg) self.assertEqual(alignment.shape, (2, 4000), msg=msg) self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=msg ) if bedN >= 6: self.assertGreater( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=msg, ) else: self.assertLess( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=msg, ) self.assertEqual(len(alignment), 2, msg=msg) self.assertIs(alignment.sequences[0], alignment.target, msg=msg) self.assertIs(alignment.sequences[1], alignment.query, msg=msg) self.assertEqual(alignment.target.id, "chr22", msg=msg) if bedN >= 4: self.assertEqual(alignment.query.id, "mRNA2", msg=msg) else: self.assertIsNone(alignment.query.id, msg=msg) if bedN == 12: self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[2000, 2433, 5601, 6000], [ 832, 399, 399, 0]]) # fmt: on ), msg=msg, ) elif bedN >= 6: self.assertTrue( np.array_equal( alignment.coordinates, np.array([[2000, 6000], [4000, 0]]), ), msg=msg, ) else: self.assertTrue( np.array_equal( alignment.coordinates, np.array([[2000, 6000], [0, 4000]]), ), msg=msg, ) if bedN >= 7: self.assertEqual(alignment.thickStart, 2300, msg=msg) if bedN >= 8: self.assertEqual(alignment.thickEnd, 5960, msg=msg) if bedN >= 9: self.assertEqual(alignment.itemRgb, "0,255,0", msg=msg) with self.assertRaises(StopIteration) as cm: next(alignments) self.fail("More than two alignments reported") def test_reading(self): """Test parsing alignments in file formats BED3 through BED12.""" for bedN in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.bb" % bedN path = os.path.join("Blat", filename) alignments = Align.parse(path, "bigbed") msg = "bed%d" % bedN self.check_autosql(alignments.declaration, bedN, msg) self.check_alignments(alignments, bedN, msg) def test_writing(self): """Test Writing alignments in file formats BED3 through BED12.""" for bedN in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.bb" % bedN path = os.path.join("Blat", filename) alignments = Align.parse(path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed", bedN=bedN) output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") msg = "bed%d" % bedN self.check_autosql(alignments.declaration, bedN, msg) self.check_alignments(alignments, bedN, msg) class TestAlign_extended_bed(unittest.TestCase): # The bigBed files bigbed_extended.littleendian.bb and # bigbed_extended.bigendian.bb are BED9+2 files, with nine predefined BED # fields and 2 extra (custom) fields. It was created by running # # bedToBigBed -as=bedExample2.as -type=bed9+2 -extraIndex=name,geneSymbol bedExample2.bed hg18.chrom.sizes bigbed_extended.bb # # where bedExample2.bed contains 10 lines selected from the example BED9+2 # file bedExample2.bed downloaded from UCSC # (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.bed) # and bedExample2.as the associated AutoSQL file, also downloaded from UCSC # (https://genome.ucsc.edu/goldenPath/help/examples/bedExample2.as) # declaring the nine predefined BED fields and the two extra fields # # The bigBed file bigbed_extended.littleendian.bb was generated on a # little-endian machine; the bigBed file bigbed_extended.bigendian.bb was # generated on a big-endian machine. def test_reading(self): """Test parsing bigbed_extended.bb.""" path = "Blat/bigbed_extended.littleendian.bb" alignments = Align.parse(path, "bigbed") self.assertEqual(alignments.byteorder, "<") self.check_alignments(alignments) path = "Blat/bigbed_extended.bigendian.bb" alignments = Align.parse(path, "bigbed") self.assertEqual(alignments.byteorder, ">") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table hg18KGchr7 "UCSC Genes for chr7 with color plus GeneSymbol and SwissProtID" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position of feature on chromosome" uint chromEnd; "End position of feature on chromosome" string name; "Name of gene" uint score; "Score" char[1] strand; "+ or - for strand" uint thickStart; "Coding region start" uint thickEnd; "Coding region end" uint reserved; "Green on + strand, Red on - strand" string geneSymbol; "Gene Symbol" string spID; "SWISS-PROT protein Accession number" ) """, ) self.assertEqual(len(alignments.targets), 1) self.assertEqual(alignments.targets[0].id, "chr7") self.assertEqual(len(alignments.targets[0]), 158821424) self.assertEqual(len(alignments), 10) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 60328) self.assertEqual(alignment.thickEnd, 60328) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 1241)) 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, "chr7") self.assertEqual(alignment.query.id, "uc010krx.1") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[60328, 61569], [1241, 0]])) ) self.assertEqual(alignment.annotations["geneSymbol"], ".") self.assertEqual(alignment.annotations["spID"], "PDGFA") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1241: 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, 1241) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 506606) self.assertEqual(alignment.thickEnd, 525164) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 22585)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003sir.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[503422, 526007], [22585, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "PDGFA") self.assertEqual(alignment.annotations["spID"], "P04085") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 22585: 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, 22585) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 504726) self.assertEqual(alignment.thickEnd, 525164) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 22585)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003sis.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[503422, 526007], [22585, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "PDGFA") self.assertEqual(alignment.annotations["spID"], "P04085-2") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 22585: 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, 22585) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 507195) self.assertEqual(alignment.thickEnd, 518820) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 12690)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003sit.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[506940, 519630], [12690, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "PDGFA") self.assertEqual(alignment.annotations["spID"], "Q32M96") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 12690: 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, 12690) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 556592) self.assertEqual(alignment.thickEnd, 717668) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 162747)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003siu.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[555912, 718659], [162747, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "PRKAR1B") self.assertEqual(alignment.annotations["spID"], "Q8N422") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 162747: 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, 162747) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 556592) self.assertEqual(alignment.thickEnd, 717668) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 163357)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003siv.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[555912, 719269], [163357, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "PRKAR1B") self.assertEqual(alignment.annotations["spID"], "Q8N422") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 163357: 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, 163357) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 556592) self.assertEqual(alignment.thickEnd, 717668) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 177901)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003siw.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[555912, 733813], [177901, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "PRKAR1B") self.assertEqual(alignment.annotations["spID"], "Q8N422") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 177901: 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, 177901) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 585418) self.assertEqual(alignment.thickEnd, 585418) self.assertEqual(alignment.itemRgb, "255,0,0") self.assertEqual(alignment.shape, (2, 22329)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003six.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[585418, 607747], [22329, 0]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], ".") self.assertEqual(alignment.annotations["spID"], "PRKAR1B") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 22329: 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, 22329) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 733217) self.assertEqual(alignment.thickEnd, 791816) self.assertEqual(alignment.itemRgb, "0,255,0") self.assertEqual(alignment.shape, (2, 59779)) 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, "chr7") self.assertEqual(alignment.query.id, "uc003siz.2") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[732863, 792642], [0, 59779]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], ".") self.assertEqual(alignment.annotations["spID"], "DKFZp762F1415") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 59779: 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, 59779) alignment = next(alignments) self.assertEqual(alignment.score, 0) self.assertEqual(alignment.thickStart, 732883) self.assertEqual(alignment.thickEnd, 791816) self.assertEqual(alignment.itemRgb, "0,255,0") self.assertEqual(alignment.shape, (2, 59779)) 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, "chr7") self.assertEqual(alignment.query.id, "uc010krz.1") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[732863, 792642], [0, 59779]]) ) ) self.assertEqual(alignment.annotations["geneSymbol"], "HEATR2") self.assertEqual(alignment.annotations["spID"], "Q86Y56") counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 59779: 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, 59779) def test_writing(self): """Test writing bigbed_extended.bb.""" byteorder = sys.byteorder # "little" or "big" path = f"Blat/bigbed_extended.{byteorder}endian.bb" with open(path, "rb") as stream: correct = stream.read() alignments = Align.parse(path, "bigbed") with open("Blat/bedExample2.as") as stream: autosql_data = stream.read() declaration = bigbed.AutoSQLTable.from_string(autosql_data) with tempfile.TemporaryFile() as output: Align.write( alignments, output, "bigbed", bedN=9, declaration=declaration, extraIndex=["name", "geneSymbol"], ) output.flush() output.seek(0) data = output.read() self.assertEqual(correct, data) alignments = Align.parse(path, "bigbed") targets = alignments.targets with tempfile.TemporaryFile() as output: Align.write( alignments, output, "bigbed", bedN=9, declaration=declaration, targets=targets, extraIndex=["name", "geneSymbol"], ) output.flush() output.seek(0) data = output.read() self.assertEqual(correct, data) class TestAlign_searching(unittest.TestCase): path = "Blat/bigbedtest.bb" # The bigBed file bigbedtest.bb 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 - def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" ) """, ) self.assertEqual(len(alignments.targets), 3) self.assertEqual(alignments.targets[0].id, "chr1") self.assertEqual(len(alignments.targets[0]), 1000) self.assertEqual(alignments.targets[1].id, "chr2") self.assertEqual(len(alignments.targets[1]), 2000) self.assertEqual(alignments.targets[2].id, "chr3") self.assertEqual(len(alignments.targets[2]), 1000) self.assertEqual(len(alignments), 8) alignment = next(alignments) self.assertEqual(alignment.score, 1) self.assertEqual(alignment.shape, (2, 90)) 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, "name1") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[10, 100], [0, 90]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 90: 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, 90) alignment = next(alignments) self.assertEqual(alignment.score, 2) self.assertEqual(alignment.shape, (2, 10)) 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, "name2") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[29, 39], [10, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 10: 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, 10) alignment = next(alignments) self.assertEqual(alignment.score, 3) self.assertEqual(alignment.shape, (2, 100)) 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, "name3") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[200, 300], [0, 100]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 100: 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, 100) alignment = next(alignments) self.assertEqual(alignment.score, 6) self.assertEqual(alignment.shape, (2, 0)) 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, "name4") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[50, 50], [0, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 0: 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, 0) self.assertEqual(counts.identities, 0) self.assertEqual(counts.mismatches, 0) alignment = next(alignments) self.assertEqual(alignment.score, 4) self.assertEqual(alignment.shape, (2, 10)) 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, "name5") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[100, 110], [0, 10]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 10: 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, 10) alignment = next(alignments) self.assertEqual(alignment.score, 5) self.assertEqual(alignment.shape, (2, 10)) 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, "name6") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[200, 210], [0, 10]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 10: 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, 10) alignment = next(alignments) self.assertEqual(alignment.score, 6) self.assertEqual(alignment.shape, (2, 0)) 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, "name7") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[220, 220], [0, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 0: 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, 0) self.assertEqual(counts.identities, 0) self.assertEqual(counts.mismatches, 0) alignment = next(alignments) self.assertEqual(alignment.score, 7) self.assertEqual(alignment.shape, (2, 0)) 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, "name8") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 0], [0, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 0: 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, 0) self.assertEqual(counts.identities, 0) self.assertEqual(counts.mismatches, 0) def test_reading(self): """Test reading bigbedtest.bb.""" alignments = Align.parse(self.path, "bigbed") self.check_alignments(alignments) def test_writing(self): """Test writing bigbedtest.bb.""" alignments = Align.parse(self.path, "bigbed") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigbed", bedN=6) output.flush() output.seek(0) alignments = Align.parse(output, "bigbed") self.check_alignments(alignments) def test_search_chromosome(self): alignments = Align.parse(self.path, "bigbed") self.assertEqual( str(alignments.declaration), """\ table bed "Browser Extensible Data" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" string name; "Name of item." uint score; "Score (0-1000)" char[1] strand; "+ or - for strand" ) """, ) 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): alignments = Align.parse(self.path, "bigbed") 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): alignments = Align.parse(self.path, "bigbed") 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.""" alignments1 = Align.parse(self.path, "bigbed") 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) class BinaryTestBaseClass(unittest.TestCase): def assertBinaryEqual(self, file1, file2): blocksize = 1024 n = 0 while True: data1 = file1.read(blocksize) data2 = file2.read(blocksize) if data1 == b"" and data2 == b"": return n1 = len(data1) if data1 == data2: n += n1 continue n2 = len(data2) if n1 < n2: return self.fail(f"unequal file sizes: {n1} bytes vs >= {n2} bytes") if n1 > n2: return self.fail(f"unequal file sizes: >= {n1} bytes vs {n2} bytes") for i, (c1, c2) in enumerate(zip(data1, data2)): if c1 != c2: return self.fail(f"bytes at position {n + i} differ: {c1} vs {c2}") @unittest.skipUnless(big is True, "big file; use --big to run") class TestAlign_big(BinaryTestBaseClass): # BED files were downloaded from the UCSC table browser: # # ucsc.bed contains the GENCODE V43 Basic gene annotations for human genome # assembly hg38. # # anoGam3.bed contains the AUGUSTUS gene annotations for genome assembly # anoGam3 of Anopheles gambiae (African malaria mosquito). # # ailMel1.bed contains the NCBI RefSeq All gene annotations for genome # assembly ailMel1 of Ailuropoda melanoleuca (giant panda). # # bisBis1.bed contains the AUGUSTUS gene annotations for genome assembly # bisBis1 of Bison bison bison (American bison). # # bigBed files were generated using bedToBigBed v. 2.9 found in # jksrc.v445.zip of the 'kent' source tree provided by UCSC # (http://hgdownload.cse.ucsc.edu/admin/). def test_a_compressed(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # bedToBigBed -as=Blat/bed12.as ucsc.clean.bed Align/hg38.chrom.sizes ucsc.bb with open("Blat/bed12.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_b_uncompressed(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # bedToBigBed -as=Blat/bed12.as -unc ucsc.clean.bed Align/hg38.chrom.sizes ucsc.unc.bb with open("Blat/bed12.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.unc.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", declaration=declaration, compress=False, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_c_bed3(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-3 ucsc.clean.bed > ucsc.bed3.bed # bedToBigBed -as=Blat/bed3.as -type=bed3 ucsc.bed3.bed Align/hg38.chrom.sizes ucsc.bed3.bb with open("Blat/bed3.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed3.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=3, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_d_bed4(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-4 ucsc.clean.bed > ucsc.bed4.bed # bedToBigBed -as=Blat/bed4.as -type=bed4 ucsc.bed4.bed Align/hg38.chrom.sizes ucsc.bed4.bb with open("Blat/bed4.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed4.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=4, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_e_bed5(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-5 ucsc.clean.bed > ucsc.bed5.bed # bedToBigBed -as=Blat/bed5.as -type=bed5 ucsc.bed5.bed Align/hg38.chrom.sizes ucsc.bed5.bb with open("Blat/bed5.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed5.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=5, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_f_bed6(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-6 ucsc.clean.bed > ucsc.bed6.bed # bedToBigBed -as=Blat/bed6.as -type=bed6 ucsc.bed6.bed Align/hg38.chrom.sizes ucsc.bed6.bb with open("Blat/bed6.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed6.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=6, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_g_bed7(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-7 ucsc.clean.bed > ucsc.bed7.bed # bedToBigBed -as=Blat/bed7.as -type=bed7 ucsc.bed7.bed Align/hg38.chrom.sizes ucsc.bed7.bb with open("Blat/bed7.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed7.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=7, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_h_bed8(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-8 ucsc.clean.bed > ucsc.bed8.bed # bedToBigBed -as=Blat/bed8.as -type=bed8 ucsc.bed8.bed Align/hg38.chrom.sizes ucsc.bed8.bb with open("Blat/bed8.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed8.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=8, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_i_bed9(self): # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -k1,1 -k2,2n ucsc.clean.bed -o ucsc.clean.bed # cut -f 1-9 ucsc.clean.bed > ucsc.bed9.bed # bedToBigBed -as=Blat/bed9.as -type=bed9 ucsc.bed9.bed Align/hg38.chrom.sizes ucsc.bed9.bb with open("Blat/bed9.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.bb" alignments = Align.parse(bigBedFileName, "bigbed") bigBedFileName = "ucsc.bed9.bb" with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", bedN=9, declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_j_extraindex(self): # If the names in the BED file are not unique, the binary contents of # the generated bigBed file will depend on the exact implementation of # the quicksort algorithm in the Standard Library of C (used by # bedToBigBed) and the quicksort algorithm in numpy (used by Biopython). # To prevent spurious errors when comparing bigBed files created by # bedToBigBed and by Biopython, we first remove lines with duplicated # names from the BED file. # grep -E -v 'fix|alt' Blat/ucsc.bed > ucsc.clean.bed # sort -u -k4,4 ucsc.clean.bed | sort -k1,1 -k2,2n > ucsc.unique.bed # bedToBigBed -as=Blat/bed12.as -extraIndex=name ucsc.unique.bed Align/hg38.chrom.sizes ucsc.indexed.bb with open("Blat/bed12.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ucsc.indexed.bb" alignments = Align.parse(bigBedFileName, "bigbed") with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", declaration=declaration, extraIndex=["name"], ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_k_anogam(self): # sort -k1,1 -k2,2n Blat/anoGam3.bed -o anoGam3.bed # bedToBigBed -as=Blat/bed12.as anoGam3.bed Blat/anoGam3.chrom.sizes anoGam3.bb with open("Blat/bed12.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "anoGam3.bb" alignments = Align.parse(bigBedFileName, "bigbed") with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_l_ailmel(self): # sort -k1,1 -k2,2n Blat/ailMel1.bed -o ailMel1.bed # bedToBigBed -as=Blat/bed12.as ailMel1.bed Blat/ailMel1.chrom.sizes ailMel1.bb with open("Blat/bed12.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "ailMel1.bb" alignments = Align.parse(bigBedFileName, "bigbed") with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) def test_m_bisbis(self): # sort -k1,1 -k2,2n bisBis1.bed -o bisBis1.bed # bedToBigBed -as=Blat/bed12.as bisBis1.bed Blat/bisBis1.chrom.sizes bisBis1.bb with open("Blat/bed12.as") as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) bigBedFileName = "bisBis1.bb" alignments = Align.parse(bigBedFileName, "bigbed") with tempfile.TemporaryFile() as output, open(bigBedFileName, "rb") as stream: Align.write( alignments, output, "bigbed", declaration=declaration, compress=True, ) output.flush() output.seek(0) self.assertBinaryEqual(output, stream) class TestDeclarations(unittest.TestCase): def test_declarations(self): for length in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.as" % length path = os.path.join("Blat", filename) with open(path) as stream: data = stream.read() declaration = bigbed.AutoSQLTable.from_string(data) self.assertEqual(declaration.name, "bed", msg=filename) self.assertEqual( declaration.comment, "Browser Extensible Data", msg=filename ) self.assertEqual(len(declaration), length, msg=filename) field = declaration[0] self.assertEqual(field.as_type, "string", msg=filename) self.assertEqual(field.name, "chrom", msg=filename) self.assertEqual( field.comment, "Reference sequence chromosome or scaffold", msg=filename ) field = declaration[1] self.assertEqual(field.as_type, "uint", msg=filename) self.assertEqual(field.name, "chromStart", msg=filename) self.assertEqual( field.comment, "Start position in chromosome", msg=filename ) field = declaration[2] self.assertEqual(field.as_type, "uint", msg=filename) self.assertEqual(field.name, "chromEnd", msg=filename) self.assertEqual(field.comment, "End position in chromosome", msg=filename) if length == 3: return field = declaration[3] self.assertEqual(field.as_type, "string", msg=filename) self.assertEqual(field.name, "name", msg=filename) self.assertEqual(field.comment, "Name of item.", msg=filename) if length == 4: return field = declaration[4] self.assertEqual(field.as_type, "uint", msg=filename) self.assertEqual(field.name, "score", msg=filename) self.assertEqual(field.comment, "Score (0-1000)", msg=filename) if length == 5: return field = declaration[5] self.assertEqual(field.as_type, "char[1]", msg=filename) self.assertEqual(field.name, "strand", msg=filename) self.assertEqual(field.comment, "+ or - for strand", msg=filename) if length == 6: return field = declaration[6] self.assertEqual(field.as_type, "uint", msg=filename) self.assertEqual(field.name, "thickStart", msg=filename) self.assertEqual( field.comment, "Start of where display should be thick (start codon)", msg=filename, ) if length == 7: return field = declaration[7] self.assertEqual(field.as_type, "uint", msg=filename) self.assertEqual(field.name, "thickEnd", msg=filename) self.assertEqual( field.comment, "End of where display should be thick (stop codon)", msg=filename, ) if length == 8: return field = declaration[8] self.assertEqual(field.as_type, "uint", msg=filename) self.assertEqual(field.name, "reserved", msg=filename) self.assertEqual( field.comment, "Used as itemRgb as of 2004-11-22", msg=filename ) if length == 9: return field = declaration[9] self.assertEqual(field.as_type, "int", msg=filename) self.assertEqual(field.name, "blockCount", msg=filename) self.assertEqual(field.comment, "Number of blocks", msg=filename) field = declaration[10] self.assertEqual(field.as_type, "int[blockCount]", msg=filename) self.assertEqual(field.name, "blockSizes", msg=filename) self.assertEqual( field.comment, "Comma separated list of block sizes", msg=filename ) field = declaration[11] self.assertEqual(field.as_type, "int[blockCount]", msg=filename) self.assertEqual(field.name, "chromStarts", msg=filename) self.assertEqual( field.comment, "Start positions relative to chromStart", msg=filename ) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)