コード例 #1
0
    def test_draw_layout_single_genomic(self):
        d = DiagramSettings()
        d1 = protein.Domain('first', [(55, 61), (71, 73)])
        d2 = protein.Domain('second', [(10, 20), (30, 34)])
        g1 = genomic.Gene('1', 150, 1000, strand=STRAND.POS)
        g2 = genomic.Gene('1', 5000, 7500, strand=STRAND.POS)
        t1 = build_transcript(
            gene=g1,
            cds_start=50,
            cds_end=249,
            exons=[(200, 299), (400, 499), (700, 899)],
            domains=[d2, d1],
        )
        t2 = build_transcript(
            gene=g2,
            cds_start=20,
            cds_end=500,
            exons=[(5100, 5299), (5800, 6199), (6500, 6549), (6700, 6799)],
            domains=[],
        )
        b1 = Breakpoint('1', 350, orient=ORIENT.LEFT)
        b2 = Breakpoint('1', 6500, orient=ORIENT.RIGHT)
        bpp = BreakpointPair(b1,
                             b2,
                             opposing_strands=False,
                             untemplated_seq='')
        ann = variant.Annotation(bpp,
                                 transcript1=t1,
                                 transcript2=t2,
                                 event_type=SVTYPE.DEL,
                                 protocol=PROTOCOL.GENOME)
        ann.add_gene(genomic.Gene('1', 1500, 1950, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('1', 3000, 3980, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('1', 3700, 4400, strand=STRAND.NEG))

        reference_genome = {'1': MockObject(seq=MockString('A'))}

        ft = variant.FusionTranscript.build(ann, reference_genome)
        ann.fusion = ft
        self.assertEqual(t1.exons[0], ft.exon_mapping[ft.exons[0].position])
        self.assertEqual(t2.exons[2], ft.exon_mapping[ft.exons[1].position])
        self.assertEqual(t2.exons[3], ft.exon_mapping[ft.exons[2].position])

        canvas, legend = draw_sv_summary_diagram(d, ann)
        self.assertEqual(5, len(canvas.elements))  # defs counts as element

        expected_height = (d.top_margin + d.bottom_margin + d.track_height +
                           d.breakpoint_bottom_margin +
                           d.breakpoint_top_margin + d.inner_margin +
                           d.track_height + d.splice_height +
                           d.breakpoint_bottom_margin +
                           d.breakpoint_top_margin + d.padding +
                           d.translation_track_height + d.padding * 2 +
                           d.domain_track_height * 2 + d.inner_margin +
                           d.track_height + d.splice_height)
        self.assertEqual(expected_height, canvas.attribs['height'])
        if OUTPUT_SVG:
            canvas.saveas('test_draw_layout_single_genomic.svg')
コード例 #2
0
    def test_draw_layout_translocation(self):
        d = DiagramSettings(domain_name_regex_filter=r'.*')
        d1 = protein.Domain('first', [(55, 61), (71, 73)])
        d2 = protein.Domain('second', [(10, 20), (30, 34)])
        g1 = genomic.Gene('1', 150, 1000, strand=STRAND.POS)
        g2 = genomic.Gene('2', 5000, 7500, strand=STRAND.NEG)
        t1 = build_transcript(
            gene=g1,
            cds_start=50,
            cds_end=249,
            exons=[(200, 299), (400, 499), (700, 899)],
            domains=[d2, d1],
        )
        t2 = build_transcript(
            gene=g2,
            cds_start=120,
            cds_end=700,
            exons=[(5100, 5299), (5800, 6199), (6500, 6549), (6700, 6799)],
            domains=[],
        )
        b1 = Breakpoint('1', 350, orient=ORIENT.LEFT)
        b2 = Breakpoint('2', 6520, orient=ORIENT.LEFT)
        bpp = BreakpointPair(b1, b2, opposing_strands=True, untemplated_seq='')
        ann = variant.Annotation(bpp,
                                 transcript1=t1,
                                 transcript2=t2,
                                 event_type=SVTYPE.ITRANS,
                                 protocol=PROTOCOL.GENOME)
        # genes 1
        ann.add_gene(genomic.Gene('1', 1500, 1950, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('1', 3000, 3980, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('1', 3700, 4400, strand=STRAND.NEG))
        # genes 2
        ann.add_gene(genomic.Gene('2', 1500, 1950, strand=STRAND.NEG))
        ann.add_gene(genomic.Gene('2', 5500, 9000, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('2', 3700, 4400, strand=STRAND.NEG))

        reference_genome = {
            '1': MockObject(seq=MockString('A')),
            '2': MockObject(seq=MockString('A')),
        }

        ft = variant.FusionTranscript.build(ann, reference_genome)
        ann.fusion = ft
        canvas, legend = draw_sv_summary_diagram(d, ann)
        assert len(canvas.elements) == 6  # defs counts as element
        expected_height = (
            d.top_margin + d.bottom_margin + d.track_height * 2 + d.padding +
            d.breakpoint_bottom_margin + d.breakpoint_top_margin +
            d.inner_margin + d.track_height + d.splice_height +
            d.breakpoint_bottom_margin + d.breakpoint_top_margin + d.padding +
            d.translation_track_height + d.padding * 2 +
            d.domain_track_height * 2 + d.inner_margin + d.track_height +
            d.splice_height)
        assert canvas.attribs['height'] == expected_height
コード例 #3
0
    def test_draw_layout_single_transcript(self):
        d = DiagramSettings()
        d1 = protein.Domain('first', [(55, 61), (71, 73)])
        d2 = protein.Domain('second', [(10, 20), (30, 34)])
        g1 = genomic.Gene('1', 150, 1000, strand=STRAND.POS)
        t = build_transcript(g1, [(200, 299), (400, 499), (700, 899)], 50, 249,
                             [d2, d1])
        b1 = Breakpoint('1', 350, orient=ORIENT.RIGHT)
        b2 = Breakpoint('1', 600, orient=ORIENT.LEFT)
        bpp = BreakpointPair(b1,
                             b2,
                             opposing_strands=False,
                             untemplated_seq='')
        ann = variant.Annotation(bpp,
                                 transcript1=t,
                                 transcript2=t,
                                 event_type=SVTYPE.DUP,
                                 protocol=PROTOCOL.GENOME)
        ann.add_gene(genomic.Gene('1', 1500, 1950, strand=STRAND.POS))

        reference_genome = {'1': MockObject(seq=MockString('A'))}
        ft = variant.FusionTranscript.build(ann, reference_genome)
        ann.fusion = ft
        canvas, legend = draw_sv_summary_diagram(d, ann)
        self.assertEqual(4, len(canvas.elements))  # defs counts as element
        expected_height = (d.top_margin + d.bottom_margin + d.track_height +
                           d.breakpoint_bottom_margin +
                           d.breakpoint_top_margin + d.inner_margin +
                           d.track_height + d.splice_height + d.padding +
                           d.translation_track_height + d.padding * 2 +
                           d.domain_track_height * 2 + d.inner_margin +
                           d.track_height + d.breakpoint_bottom_margin +
                           d.breakpoint_top_margin + d.splice_height)
        if OUTPUT_SVG:
            canvas.saveas('test_draw_layout_single_transcript.svg')
        self.assertEqual(expected_height, canvas.attribs['height'])
コード例 #4
0
    def test_draw_translocation_with_template(self):
        d = DiagramSettings()
        d1 = protein.Domain('PF0001', [(55, 61), (71, 73)])
        d2 = protein.Domain('PF0002', [(10, 20), (30, 34)])
        g1 = genomic.Gene(TEMPLATE_METADATA['1'],
                          150,
                          1000,
                          strand=STRAND.POS,
                          aliases=['HUGO2'])
        g2 = genomic.Gene(TEMPLATE_METADATA['X'],
                          5000,
                          7500,
                          strand=STRAND.NEG,
                          aliases=['HUGO3'])
        t1 = build_transcript(
            gene=g1,
            name='transcript1',
            cds_start=50,
            cds_end=249,
            exons=[(200, 299), (400, 499), (700, 899)],
            domains=[d2, d1],
        )
        t2 = build_transcript(
            gene=g2,
            name='transcript2',
            cds_start=120,
            cds_end=700,
            exons=[(5100, 5299), (5800, 6199), (6500, 6549), (6700, 6799)],
            domains=[],
        )
        b1 = Breakpoint('1', 350, orient=ORIENT.LEFT)
        b2 = Breakpoint('2', 6520, orient=ORIENT.LEFT)
        bpp = BreakpointPair(b1, b2, opposing_strands=True, untemplated_seq='')
        ann = variant.Annotation(bpp,
                                 transcript1=t1,
                                 transcript2=t2,
                                 event_type=SVTYPE.ITRANS,
                                 protocol=PROTOCOL.GENOME)
        # genes 1
        ann.add_gene(
            genomic.Gene('1', 1500, 1950, strand=STRAND.POS,
                         aliases=['HUGO5']))
        ann.add_gene(genomic.Gene('1', 3000, 3980, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('1', 3700, 4400, strand=STRAND.NEG))
        # genes 2
        ann.add_gene(genomic.Gene('2', 1500, 1950, strand=STRAND.NEG))
        ann.add_gene(genomic.Gene('2', 5500, 9000, strand=STRAND.POS))
        ann.add_gene(genomic.Gene('2', 3700, 4400, strand=STRAND.NEG))

        reference_genome = {
            '1': MockObject(seq=MockString('A')),
            '2': MockObject(seq=MockString('A')),
        }

        ft = variant.FusionTranscript.build(ann, reference_genome)
        ann.fusion = ft
        canvas, legend = draw_sv_summary_diagram(d,
                                                 ann,
                                                 draw_reference_templates=True,
                                                 templates=TEMPLATE_METADATA)
        if OUTPUT_SVG:
            canvas.saveas('test_draw_translocation_with_template.svg')
        self.assertEqual(8, len(canvas.elements))  # defs counts as element
        expected_height = (
            d.top_margin + d.bottom_margin + d.track_height * 2 + d.padding +
            d.breakpoint_bottom_margin + d.breakpoint_top_margin +
            d.inner_margin + d.track_height + d.splice_height +
            d.breakpoint_bottom_margin + d.breakpoint_top_margin + d.padding +
            d.translation_track_height + d.padding * 2 +
            d.domain_track_height * 2 + d.inner_margin * 2 + d.track_height +
            d.breakpoint_bottom_margin + d.breakpoint_top_margin +
            d.splice_height + d.template_track_height)
        self.assertAlmostEqual(expected_height, canvas.attribs['height'])