def test_consensus():
""" Consensus sequences have a different name format.
They also need to have the parentheses replaced by brackets so they don't
get dropped from the tree file.
"""
raw_hcv = StringIO("""\
>Ref.CON_1a(142)
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.CON_1a[142]-1a
ACTAGGA
GAGATTT
>Ref.2b.Bar-2b
TAGACT
"""
filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
def test_consensus():
""" Consensus sequences have a different name format.
They also need to have the parentheses replaced by brackets so they don't
get dropped from the tree file.
"""
raw_hcv = StringIO("""\
>Ref.CON_1a(142)
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.CON_1a[142]-1a
ACTAGGA
GAGATTT
>Ref.2b.Bar-2b
TAGACT
"""
filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
def test_filter_duplicates():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
>Ref.1a.Foo
AAA
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
>Ref.2b.Bar-2b
TAGACT
"""
expected_invalid_headers = ['>Ref.1a.Foo (duplicate)']
invalid_headers = filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
assert expected_invalid_headers == invalid_headers
def test_filter_duplicates():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
>Ref.1a.Foo
AAA
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
>Ref.2b.Bar-2b
TAGACT
"""
expected_invalid_headers = ['>Ref.1a.Foo (duplicate)']
invalid_headers = filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
assert expected_invalid_headers == invalid_headers
def test_add_subtype():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
>Ref.2b.Bar-2b
TAGACT
"""
filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
def test_add_subtype():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
>Ref.2b.Bar-2b
TAGACT
"""
filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
def test_filter_missing_subtype():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2.Bar
TAGACT
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
"""
expected_invalid_headers = ['>Ref.2.Bar']
invalid_headers = filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
assert expected_invalid_headers == invalid_headers
def test_filter_missing_subtype():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2.Bar
TAGACT
""")
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
"""
expected_invalid_headers = ['>Ref.2.Bar']
invalid_headers = filter_hcv_fasta(raw_hcv, filtered_hcv)
assert expected_filtered_hcv == filtered_hcv.getvalue()
assert expected_invalid_headers == invalid_headers
def test_filter_exclusions():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
""")
excluded = ['Bar']
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
"""
expected_invalid_headers = ['>Ref.2b.Bar (excluded)']
invalid_headers = filter_hcv_fasta(raw_hcv, filtered_hcv, excluded)
assert expected_filtered_hcv == filtered_hcv.getvalue()
assert expected_invalid_headers == invalid_headers
def test_filter_exclusions():
raw_hcv = StringIO("""\
>Ref.1a.Foo
ACTAGGA
GAGATTT
>Ref.2b.Bar
TAGACT
""")
excluded = ['Bar']
filtered_hcv = StringIO()
expected_filtered_hcv = """\
>Ref.1a.Foo-1a
ACTAGGA
GAGATTT
"""
expected_invalid_headers = ['>Ref.2b.Bar (excluded)']
invalid_headers = filter_hcv_fasta(raw_hcv, filtered_hcv, excluded)
assert expected_filtered_hcv == filtered_hcv.getvalue()
assert expected_invalid_headers == invalid_headers