def test_summarize_zero_coverage():
figure = Figure()
figure.add(Coverage(10, 20, [0, 0, 0]), gap=-4)
figure.add(Track(10, 20, label="Bar"))
with pytest.raises(ZeroDivisionError):
summarize_figure(figure)
def test_plot_genome_coverage_gap():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HCV-1a,HCV-1a,1,1,0,0,5
1-HCV-1a,HCV-1a,2,2,0,0,5
1-HCV-1a,HCV-1a,4,4,0,0,6
1-HCV-1a,HCV-1a,5,5,0,0,6
1-HCV-1a,HCV-1a,6,6,0,0,6
contig-1-HCV-1a,HCV-1a,1,1,0,,
contig-1-HCV-1a,HCV-1a,2,2,0,,
contig-1-HCV-1a,HCV-1a,4,4,0,,
contig-1-HCV-1a,HCV-1a,5,5,0,,
contig-1-HCV-1a,HCV-1a,6,6,0,,
""")
expected_figure = """\
5'[1-341], C[342-914], E1[915-1490], E2[1491-2579], p7[2580-2768], \
NS2[2769-3419], NS3[3420-5312], NS4b[5475-6257], NS4a[5313-5474], \
NS5a[6258-7601], NS5b[7602-9374], 3'[9375-9646]
Coverage 5x2, 0, 6x3
[1-2], [4-6], 1-HCV-1a - depth 6(1-9646)
[1-2], [4-6], contig-1-HCV-1a(1-9646)
"""
figure = build_coverage_figure(genome_coverage_csv)
assert expected_figure == summarize_figure(figure)
def test_plot_genome_coverage_insertion():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HCV-1a,HCV-1a,1,1,0,0,5
1-HCV-1a,HCV-1a,2,2,0,0,5
1-HCV-1a,HCV-1a,3,3,0,0,5
1-HCV-1a,HCV-1a,4,,0,0,6
1-HCV-1a,HCV-1a,5,,0,0,6
1-HCV-1a,HCV-1a,6,,0,0,6
1-HCV-1a,HCV-1a,7,4,0,0,7
1-HCV-1a,HCV-1a,8,5,0,0,7
1-HCV-1a,HCV-1a,9,6,0,0,7
1-HCV-1a,HCV-1a,10,7,0,0,8
1-HCV-1a,HCV-1a,11,8,0,0,8
1-HCV-1a,HCV-1a,12,9,0,0,8
""")
expected_figure = """\
5'[1-341], C[342-914], E1[915-1490], E2[1491-2579], p7[2580-2768], \
NS2[2769-3419], NS3[3420-5312], NS4b[5475-6257], NS4a[5313-5474], \
NS5a[6258-7601], NS5b[7602-9374], 3'[9375-9646]
Coverage 5x3, 7x3, 8x3
[1-9], 1-HCV-1a - depth 8(1-9646), lightgreen{4-6}
"""
figure = build_coverage_figure(genome_coverage_csv)
assert expected_figure == summarize_figure(figure)
def test_plot_genome_coverage_unmapped():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage,link
1-HCV-1a,HCV-1a,1,1,0,0,5,M
1-HCV-1a,HCV-1a,2,2,0,0,5,M
1-HCV-1a,HCV-1a,3,3,0,0,5,M
1-HCV-1a,HCV-1a,4,4,0,0,6,M
1-HCV-1a,HCV-1a,5,5,0,0,6,U
1-HCV-1a,HCV-1a,6,6,0,0,6,U
1-HCV-1a,HCV-1a,7,7,0,0,7,U
1-HCV-1a,HCV-1a,8,8,0,0,7,U
1-HCV-1a,HCV-1a,9,9,0,0,7,U
1-HCV-1a,HCV-1a,10,10,0,0,8,M
1-HCV-1a,HCV-1a,11,11,0,0,8,M
1-HCV-1a,HCV-1a,12,12,0,0,8,M
""")
expected_figure = """\
5'[1-341], C[342-914], E1[915-1490], E2[1491-2579], p7[2580-2768], \
NS2[2769-3419], NS3[3420-5312], NS4b[5475-6257], NS4a[5313-5474], \
NS5a[6258-7601], NS5b[7602-9374], 3'[9375-9646]
Coverage 5x3, 6x3, 7x3, 8x3
[1-12], 1-HCV-1a - depth 8(1-9646), yellow{5-9}
"""
figure = build_coverage_figure(genome_coverage_csv)
assert summarize_figure(figure) == expected_figure
def test_plot_genome_coverage_minimap():
""" Replace BLAST results with minimap2. """
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HCV-1a,HCV-1a,1,8001,0,0,5
1-HCV-1a,HCV-1a,2,8002,0,0,5
1-HCV-1a,HCV-1a,3,8003,0,0,7
1-HCV-1a,HCV-1a,4,8004,0,0,5
1-HCV-1a,HCV-1a,5,8005,0,0,5
1-HCV-1a,HCV-1a,6,8006,0,0,5
""")
minimap_hits_csv = StringIO("""\
contig,ref_name,score,match,pident,start,end,ref_start,ref_end
1-HCV-1a,HCV-1a,40,0.33,100,5,6,7006,7005
1-HCV-1a,HCV-1a,50,0.5,100,1,3,8001,8003
""")
expected_figure = """\
5'[1-341], C[342-914], E1[915-1490], E2[1491-2579], p7[2580-2768], \
NS2[2769-3419], NS3[3420-5312], NS4b[5475-6257], NS4a[5313-5474], \
NS5a[6258-7601], NS5b[7602-9374], 3'[9375-9646]
7005<-1.2--7006, 8001--1.1->8003
8001--1.1->8003, 8005--1.2->8006
Coverage 5x2, 7, 5x3
[8001-8006], 1-HCV-1a - depth 7(1-9646)
"""
figure = build_coverage_figure(genome_coverage_csv, minimap_hits_csv)
assert summarize_figure(figure) == expected_figure
def test_plot_genome_coverage_blast_aligns_refs():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,1,2261,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,2,2262,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,3,2263,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,4,2264,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,5,2265,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,6,2266,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,7,2267,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,8,2268,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,9,2269,0,0,5
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,10,2270,0,0,5
""")
blast_csv = StringIO("""\
contig_num,ref_name,score,match,pident,start,end,ref_start,ref_end
1,HIV1-G-CM-KP718923-seed,300,1,90,1,10,1653,1662
""")
expected_figure = """\
5' LTR[1-634], gag[789-2289], vif[5040-5616], tat[8379-8469], nef[8796-9414]
tat[5831-6045], vpu[6061-6307], rev[8379-8653], 3' LTR[9086-9719]
pol[2085-5096], vpr[5558-5847], rev[5970-6045], env[6225-8795]
PR[2252-2549], RT[2549-3869], INT[4229-5093], V3[7109-7217], GP41[7757-8792]
2261--1.1->2270
2261--1.1->2270
Coverage 5x10
[2261-2270], 1-HIV1-G-CM-KP718923-seed - depth 5(1-9719)
"""
figure = build_coverage_figure(genome_coverage_csv, blast_csv)
assert summarize_figure(figure) == expected_figure
def test_plot_genome_coverage_blast_collision():
""" Two blast results end at the same position. """
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HCV-1a,HCV-1a,1,8001,0,0,5
1-HCV-1a,HCV-1a,2,8002,0,0,5
1-HCV-1a,HCV-1a,3,8003,0,0,7
1-HCV-1a,HCV-1a,4,8004,0,0,5
1-HCV-1a,HCV-1a,5,8005,0,0,5
1-HCV-1a,HCV-1a,6,8006,0,0,5
""")
blast_csv = StringIO("""\
contig_num,ref_name,score,match,pident,start,end,ref_start,ref_end
1,HCV-1g,30,0.33,90,1,2,5001,5002
1,HCV-1a,40,0.33,100,3,6,7003,7006
1,HCV-1a,50,0.5,100,1,6,8001,8006
""")
expected_figure = """\
5'[1-341], C[342-914], E1[915-1490], E2[1491-2579], p7[2580-2768], \
NS2[2769-3419], NS3[3420-5312], NS4b[5475-6257], NS4a[5313-5474], \
NS5a[6258-7601], NS5b[7602-9374], 3'[9375-9646]
7003--1.2->7006, 8001--1.1->8006
8001--1.1->8006, 8003--1.2->8006
Coverage 5x2, 7, 5x3
[8001-8006], 1-HCV-1a - depth 7(1-9646)
"""
figure = build_coverage_figure(genome_coverage_csv, blast_csv)
assert summarize_figure(figure) == expected_figure
def test_plot_genome_coverage_two_contigs():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,dels,coverage
1-HCV-1a,HCV-1a,1,1,0,5
1-HCV-1a,HCV-1a,2,2,0,5
1-HCV-1a,HCV-1a,3,3,0,7
1-HCV-1a,HCV-1a,4,4,0,5
1-HCV-1a,HCV-1a,5,5,0,5
1-HCV-1a,HCV-1a,6,6,0,5
contig-1-HCV-1a,HCV-1a,1,1,,
contig-1-HCV-1a,HCV-1a,2,2,,
contig-1-HCV-1a,HCV-1a,3,3,,
contig-1-HCV-1a,HCV-1a,4,4,,
contig-1-HCV-1a,HCV-1a,5,5,,
contig-1-HCV-1a,HCV-1a,6,6,,
2-HCV-1b-partial,,1,,0,5
2-HCV-1b-partial,,2,,0,5
2-HCV-1b-partial,,3,,0,29
2-HCV-1b-partial,,4,,0,5
2-HCV-1b-partial,,5,,0,5
2-HCV-1b-partial,,6,,0,5
3-HCV-1a,HCV-1a,101,101,0,15
3-HCV-1a,HCV-1a,102,102,0,15
3-HCV-1a,HCV-1a,103,103,0,17
3-HCV-1a,HCV-1a,104,104,0,15
3-HCV-1a,HCV-1a,105,105,0,15
3-HCV-1a,HCV-1a,106,106,0,15
contig-3-HCV-1a,HCV-1a,1,101,,
contig-3-HCV-1a,HCV-1a,2,102,,
contig-3-HCV-1a,HCV-1a,3,103,,
contig-3-HCV-1a,HCV-1a,4,104,,
contig-3-HCV-1a,HCV-1a,5,105,,
contig-3-HCV-1a,HCV-1a,6,106,,
""")
expected_figure = """\
5'[1-341], C[342-914], E1[915-1490], E2[1491-2579], p7[2580-2768], \
NS2[2769-3419], NS3[3420-5312], NS4b[5475-6257], NS4a[5313-5474], \
NS5a[6258-7601], NS5b[7602-9374], 3'[9375-9646]
Coverage 15x2, 17, 15x3
[101-106], 3-HCV-1a - depth 17(1-9646)
[101-106], contig-3-HCV-1a(1-9646)
Coverage 5x2, 7, 5x3
[1-6], 1-HCV-1a - depth 7(1-9646)
[1-6], contig-1-HCV-1a(1-9646)
[1-500], [1001-1500], [2001-2500], [3001-3500], [4001-4500], \
[5001-5500], [6001-6500], [7001-7500], [8001-8500], [9001-9500], \
Partial Blast Results(1-9646)
Coverage 5x2, 29, 5x3
[1-6], 2-HCV-1b-partial - depth 29(1-9646)
"""
figure = build_coverage_figure(genome_coverage_csv)
assert summarize_figure(figure) == expected_figure
def test_plot_genome_coverage_empty():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
""")
expected_figure = """\
No contigs found.(1-500)
"""
figure = build_coverage_figure(genome_coverage_csv)
assert expected_figure == summarize_figure(figure)
def test_summarize_label_objects():
figure = Figure()
figure.add(Track(0, 0, label=Label(25, "Foo:")))
figure.add(Track(0, 0, label="Bar:"))
expected_summary = """\
Foo:
Bar:
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_arrow():
figure = Figure()
figure.add(Arrow(10, 50, label='Foo'))
figure.add(Arrow(60, 30, label='Bar'))
expected_summary = """\
10--Foo->50
30<-Bar--60
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_smooth_coverage_ten_percent():
figure = Figure()
figure.add(SmoothCoverage(10, 20, [100, 110, 111, 50]), gap=-4)
figure.add(Track(12, 22, label="Bar"))
expected_summary = """\
Coverage 100x2, 111, 50
Bar[12-22]
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_smooth_coverage():
figure = Figure()
figure.add(SmoothCoverage(10, 20, [11, 11, 21, 1, 1, 1]), gap=-4)
figure.add(Track(12, 22, label="Bar"))
expected_summary = """\
Coverage 11x2, 21, 1x3
Bar[12-22]
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_labels():
figure = Figure()
figure.add(Track(1, 200, label="Foo"))
figure.add(Track(1, 200, label="Bar", color='none'))
expected_summary = """\
Foo[1-200]
Bar(1-200)
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_multitracks():
figure = Figure()
figure.add(Track(0, 0, label="Foo:"))
figure.add(
Multitrack([Track(10, 20, label="Bar"),
Track(30, 40, label="Baz")]))
expected_summary = """\
Foo:
Bar[10-20], Baz[30-40]
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_regions():
figure = Figure()
figure.add(
Track(1,
200,
label="Foo",
regions=[(50, 100, 'lightgreen'), (110, 120, 'red')]))
expected_summary = """\
Foo[1-200], lightgreen{50-100}, red{110-120}
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_add_partial_banner():
""" Last dash in the header banner can be less than 500 wide. """
figure = Figure()
add_partial_banner(figure, 0, 500)
add_partial_banner(figure, 0, 700)
add_partial_banner(figure, 0, 1200)
expected_figure = """\
[1-500], Partial Blast Results(1-500)
[1-500], Partial Blast Results(1-700)
[1-500], [1001-1200], Partial Blast Results(1-1200)
"""
assert expected_figure == summarize_figure(figure)
def test_summarize_arrow_group():
figure = Figure()
figure.add(
ArrowGroup([Arrow(10, 50, label='Foo'),
Arrow(60, 30, label='Bar')]))
figure.add(
ArrowGroup([Arrow(1, 50, label='Baz'),
Arrow(90, 100, label='Boom')]))
expected_summary = """\
10--Foo->50, 30<-Bar--60
1--Baz->50, 90--Boom->100
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_multitracks_with_separate_label():
figure = Figure()
figure.add(Track(0, 0, label="Foo:"))
figure.add(
Multitrack([
Track(10, 20),
Track(30, 40),
Track(10, 40, label="Bar", color='none')
]))
expected_summary = """\
Foo:
[10-20], [30-40], Bar(10-40)
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_plot_genome_coverage_partial_header():
""" Last dash in the header banner can be less than 500 wide. """
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
""")
genome_coverage_csv.seek(0, 2) # EOF
for i in range(1010):
genome_coverage_csv.write(f'1-HCV-1a-partial,,{i+1},,0,0,5\n')
genome_coverage_csv.seek(0)
expected_figure = """\
[1-500], [1001-1010], Partial Blast Results(1-1010)
Coverage 5x1010
[1-1010], 1-HCV-1a-partial - depth 5(1-1010)
"""
figure = build_coverage_figure(genome_coverage_csv)
assert expected_figure == summarize_figure(figure)
def test_plot_genome_coverage_zero():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,dels,coverage
1-HCV-1b-partial,,1,,0,0
1-HCV-1b-partial,,2,,0,0
1-HCV-1b-partial,,3,,0,0
1-HCV-1b-partial,,4,,0,0
1-HCV-1b-partial,,5,,0,0
1-HCV-1b-partial,,6,,0,0
""")
expected_figure = """\
[1-500], Partial Blast Results(1-500)
[1-6], 1-HCV-1b-partial(1-500)
"""
figure = build_coverage_figure(genome_coverage_csv)
assert expected_figure == summarize_figure(figure)
def test_plot_genome_coverage_partial():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HCV-1a-partial,,1,,0,0,5
1-HCV-1a-partial,,2,,0,0,5
1-HCV-1a-partial,,3,,0,0,7
1-HCV-1a-partial,,4,,0,0,5
1-HCV-1a-partial,,5,,0,0,5
1-HCV-1a-partial,,6,,0,0,5
""")
expected_figure = """\
[1-500], Partial Blast Results(1-500)
Coverage 5x2, 7, 5x3
[1-6], 1-HCV-1a-partial - depth 7(1-500)
"""
figure = build_coverage_figure(genome_coverage_csv)
assert expected_figure == summarize_figure(figure)
def test_plot_genome_coverage_offset_blast():
""" When a contig extends before the reference start, offset everything. """
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,ins,dels,coverage
1-HCV-1a,HCV-1a,1,-2,0,0,5
1-HCV-1a,HCV-1a,2,-1,0,0,5
1-HCV-1a,HCV-1a,3,0,0,0,7
1-HCV-1a,HCV-1a,4,1,0,0,5
1-HCV-1a,HCV-1a,5,2,0,0,5
1-HCV-1a,HCV-1a,6,3,0,0,5
1-HCV-1a,HCV-1a,7,,0,0,5
1-HCV-1a,HCV-1a,8,,0,0,5
1-HCV-1a,HCV-1a,9,,0,0,5
1-HCV-1a,HCV-1a,10,4,0,0,5
1-HCV-1a,HCV-1a,11,5,0,0,5
1-HCV-1a,HCV-1a,12,6,0,0,5
2-unknown-partial,,1,,0,0,6
2-unknown-partial,,2,,0,0,6
2-unknown-partial,,3,,0,0,6
""")
blast_csv = StringIO("""\
contig_num,ref_name,score,match,pident,start,end,ref_start,ref_end
1,HCV-1a,30,0.33,90,10,12,4,6
""")
expected_figure = """\
5'[4-344], C[345-917], E1[918-1493], E2[1494-2582], p7[2583-2771], \
NS2[2772-3422], NS3[3423-5315], NS4b[5478-6260], NS4a[5316-5477], \
NS5a[6261-7604], NS5b[7605-9377], 3'[9378-9649]
7--1.1->9
7--1.1->9
Coverage 5x2, 7, 5x6
[1-9], 1-HCV-1a - depth 7(1-9649), lightgreen{7-9}
[4-503], [1004-1503], [2004-2503], [3004-3503], [4004-4503], \
[5004-5503], [6004-6503], [7004-7503], [8004-8503], [9004-9503], \
Partial Blast Results(4-9649)
Coverage 6x3
[4-6], 2-unknown-partial - depth 6(1-9649)
"""
figure = build_coverage_figure(genome_coverage_csv, blast_csv)
assert summarize_figure(figure) == expected_figure
def test_plot_genome_coverage_g2p():
genome_coverage_csv = StringIO("""\
contig,coordinates,query_nuc_pos,refseq_nuc_pos,dels,coverage,link
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,1,2261,0,5,M
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,2,2262,0,5,M
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,3,2263,0,5,M
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,4,2264,0,5,M
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,5,2265,0,5,M
1-HIV1-G-CM-KP718923-seed,HIV1-B-FR-K03455-seed,6,2266,0,5,M
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,1,7201,0,100,M
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,2,7202,0,100,M
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,3,7203,0,100,M
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,4,7204,0,100,M
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,5,7205,0,100,M
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,6,7206,0,100,M
""")
minimap_hits_csv = StringIO("""\
contig,ref_name,start,end,ref_start,ref_end
1-HIV1-G-CM-KP718923-seed,HIV1-G-CM-KP718923-seed,1,10,1653,1658
HIV1-CON-XX-Consensus-seed,HIV1-B-FR-K03455-seed,1,6,7201,7206
""")
expected_figure = """\
5' LTR[1-634], gag[789-2289], vif[5040-5616], tat[8379-8469], nef[8796-9414]
tat[5831-6045], vpu[6061-6307], rev[8379-8653], 3' LTR[9086-9719]
pol[2085-5096], vpr[5558-5847], rev[5970-6045], env[6225-8795]
PR[2252-2549], RT[2549-3869], INT[4229-5093], V3[7109-7217], GP41[7757-8792]
2261--1.1->2266
Coverage 100x6
[7201-7206], HIV1-CON-XX-Consensus-seed - depth 100(1-9719)
2261--1.1->2266
Coverage 5x6
[2261-2266], 1-HIV1-G-CM-KP718923-seed - depth 5(1-9719)
"""
figure = build_coverage_figure(genome_coverage_csv, minimap_hits_csv)
assert summarize_figure(figure) == expected_figure
