Python combine_samples Beispiele

Beispiel #1

Datei: test_hcv_reference_tree.py Projekt: pastvir/MiCall

def test_combine_samples_hcv_only():
    filtered_hcv = StringIO("""\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
""")
    consensus_file = StringIO("""\
sample,region,q-cutoff,consensus-percent-cutoff,offset,sequence
2130A-HIV_S15,HIV1-B-FR-KF716496-seed,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HIV_S15,HIV1-B-FR-KF716496-seed,15,0.010,7669,TCHATGTCATACTCCTGGACAGGGGCTCTG
""")
    coverage_scores = StringIO("""\
sample,region,seed,on.score
2130A-HIV_S15,PR,HIV1-B-FR-KF716496-seed,4
""")
    combined_file = StringIO()
    expected_combined_file = """\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
"""

    combine_samples(filtered_hcv, consensus_file, coverage_scores,
                    combined_file)

    assert expected_combined_file == combined_file.getvalue()

Beispiel #2

Datei: test_hcv_reference_tree.py Projekt: pastvir/MiCall

def test_combine_samples_unused_region():
    filtered_hcv = StringIO("""\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
""")
    consensus_file = StringIO("""\
sample,region,q-cutoff,consensus-percent-cutoff,offset,sequence
2000A-HCV_S14,HCV-3c,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HCV_S15,HCV-2a,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HCV_S15,HCV-3c,15,MAX,7669,TCH-----ATACTCCTGGACAGGGGCTCTG
""")
    coverage_scores = StringIO("""\
sample,region,seed,on.score
2000A-HCV_S14,HCV3-S52-NS5a,HCV-3c,4
2130A-HCV_S15,HCV2-JFH-1-NS5a,HCV-2a,4
2130A-HCV_S15,HCV3-S52-NS4a,HCV-3c,4
""")
    combined_file = StringIO()
    expected_combined_file = """\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
>Sample.3c.2000A-HCV_S14~NS5a*-3c
TCCATGTCATACTCCTGGACAGGGGCTCTG
>Sample.2a.2130A-HCV_S15~NS5a*-2a
TCCATGTCATACTCCTGGACAGGGGCTCTG
>Sample.3c.2130A-HCV_S15~NS4a-3c
TCH-----ATACTCCTGGACAGGGGCTCTG
"""

    combine_samples(filtered_hcv, consensus_file, coverage_scores,
                    combined_file)

    assert expected_combined_file == combined_file.getvalue()

Beispiel #3

Datei: test_hcv_reference_tree.py Projekt: pastvir/MiCall

def test_combine_samples_multiple_projects():
    filtered_hcv = StringIO("""\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
""")
    consensus_file = StringIO("""\
sample,region,q-cutoff,consensus-percent-cutoff,offset,sequence
2130A-HCV_S15,HCV-2a,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HCV_S15,HCV-2a,15,0.010,7669,TCHATGTCATACTCCTGGACAGGGGCTCTG
""")
    coverage_scores = StringIO("""\
sample,region,seed,project,on.score
2130A-HCV_S15,HCV2-JFH-1-NS5a,HCV-2a,HCV,4
2130A-HCV_S15,HCV2-JFH-1-NS5a,HCV-2a,MidHCV,4
""")
    combined_file = StringIO()
    expected_combined_file = """\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
>Sample.2a.2130A-HCV_S15~NS5a*-2a
TCCATGTCATACTCCTGGACAGGGGCTCTG
"""

    combine_samples(filtered_hcv, consensus_file, coverage_scores,
                    combined_file)

    assert expected_combined_file == combined_file.getvalue()

Beispiel #4

Datei: test_hcv_reference_tree.py Projekt: cfe-lab/MiCall

def test_combine_samples_hcv_only():
    filtered_hcv = StringIO("""\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
""")
    consensus_file = StringIO("""\
sample,region,q-cutoff,consensus-percent-cutoff,offset,sequence
2130A-HIV_S15,HIV1-B-FR-KF716496-seed,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HIV_S15,HIV1-B-FR-KF716496-seed,15,0.010,7669,TCHATGTCATACTCCTGGACAGGGGCTCTG
""")
    coverage_scores = StringIO("""\
sample,region,seed,on.score
2130A-HIV_S15,PR,HIV1-B-FR-KF716496-seed,4
""")
    combined_file = StringIO()
    expected_combined_file = """\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
"""

    combine_samples(filtered_hcv, consensus_file, coverage_scores, combined_file)

    assert expected_combined_file == combined_file.getvalue()

Beispiel #5

Datei: test_hcv_reference_tree.py Projekt: cfe-lab/MiCall

def test_combine_samples_unused_region():
    filtered_hcv = StringIO("""\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
""")
    consensus_file = StringIO("""\
sample,region,q-cutoff,consensus-percent-cutoff,offset,sequence
2000A-HCV_S14,HCV-3c,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HCV_S15,HCV-2a,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HCV_S15,HCV-3c,15,MAX,7669,TCH-----ATACTCCTGGACAGGGGCTCTG
""")
    coverage_scores = StringIO("""\
sample,region,seed,on.score
2000A-HCV_S14,HCV3-S52-NS5a,HCV-3c,4
2130A-HCV_S15,HCV2-JFH-1-NS5a,HCV-2a,4
2130A-HCV_S15,HCV3-S52-NS4a,HCV-3c,4
""")
    combined_file = StringIO()
    expected_combined_file = """\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
>Sample.3c.2000A-HCV_S14~NS5a*-3c
TCCATGTCATACTCCTGGACAGGGGCTCTG
>Sample.2a.2130A-HCV_S15~NS5a*-2a
TCCATGTCATACTCCTGGACAGGGGCTCTG
>Sample.3c.2130A-HCV_S15~NS4a-3c
TCH-----ATACTCCTGGACAGGGGCTCTG
"""

    combine_samples(filtered_hcv, consensus_file, coverage_scores, combined_file)

    assert expected_combined_file == combined_file.getvalue()

Beispiel #6

Datei: test_hcv_reference_tree.py Projekt: cfe-lab/MiCall

def test_combine_samples_multiple_projects():
    filtered_hcv = StringIO("""\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
""")
    consensus_file = StringIO("""\
sample,region,q-cutoff,consensus-percent-cutoff,offset,sequence
2130A-HCV_S15,HCV-2a,15,MAX,7669,TCCATGTCATACTCCTGGACAGGGGCTCTG
2130A-HCV_S15,HCV-2a,15,0.010,7669,TCHATGTCATACTCCTGGACAGGGGCTCTG
""")
    coverage_scores = StringIO("""\
sample,region,seed,project,on.score
2130A-HCV_S15,HCV2-JFH-1-NS5a,HCV-2a,HCV,4
2130A-HCV_S15,HCV2-JFH-1-NS5a,HCV-2a,MidHCV,4
""")
    combined_file = StringIO()
    expected_combined_file = """\
>Ref.1a.Foo-1a
ACTACCTGA
TGACG
>Sample.2a.2130A-HCV_S15~NS5a*-2a
TCCATGTCATACTCCTGGACAGGGGCTCTG
"""

    combine_samples(filtered_hcv, consensus_file, coverage_scores, combined_file)

    assert expected_combined_file == combined_file.getvalue()