def test_simple(self):
fam = Family()
fam.name = "Test1"
fam.accession = "TEST0001"
fam.version = 1
fam.clades = []
fam.consensus = "ACGTAAAA"
self.assertEqual(
fam.to_fasta(None),
">Test1\nACGTAAAA\n"
)
self.assertEqual(
fam.to_fasta(None, use_accession=True),
">TEST0001.1 name=Test1\nACGTAAAA\n"
)
def test_buffer(self):
fam = Family()
fam.name = "Test6"
fam.accession = "TEST0006"
fam.version = 6
fam.clades = []
fam.consensus = "AAAAGCGCGCAAAA"
self.assertEqual(
fam.to_fasta(fakedb(), buffer=True),
">Test6#buffer\nAAAAGCGCGCAAAA\n"
)
self.assertEqual(
fam.to_fasta(fakedb(), buffer=[5, 10]),
">Test6_5_10#buffer\nGCGCGC\n"
)
def test_missing_consensus(self):
fam = Family()
fam.name = "Test8"
fam.accession = "TEST0008"
fam.version = 8
fam.clades = []
self.assertEqual(fam.to_fasta(fakedb()), None)
def test_without_version(self):
fam = Family()
fam.accession = "Test11"
fam.clades = []
fam.consensus = "acgt"
self.assertEqual(
fam.to_fasta(fakedb(), use_accession=True),
">Test11\nACGT\n"
)
def test_classname(self):
fam = Family()
fam.name = "Test2"
fam.accession = "TEST0002"
fam.version = 2
fam.clades = []
fam.consensus = "TCGATTTT"
fam.repeat_type = "Type"
self.assertEqual(
fam.to_fasta(None, include_class_in_name=True),
">Test2#Type\nTCGATTTT\n"
)
fam.repeat_subtype = "SubType"
self.assertEqual(
fam.to_fasta(None, include_class_in_name=True),
">Test2#Type/SubType\nTCGATTTT\n"
)
def test_clades(self):
fam = Family()
fam.name = "Test4"
fam.accession = "TEST0004"
fam.version = 4
fam.clades = [2, 3]
fam.consensus = "ACGT"
self.assertEqual(
fam.to_fasta(fakedb()),
">Test4 @A_Clade @Another_Clade_3.\nACGT\n"
)
def test_complement(self):
fam = Family()
fam.name = "Test3"
fam.accession = "TEST0003"
fam.version = 3
fam.clades = []
fam.consensus = "CGTAWWKSAAAA"
self.assertEqual(
fam.to_fasta(None, do_reverse_complement=True),
">Test3 (anti)\nTTTTWMSSTACG\n"
)
def test_always_exports_uppercase(self):
fam = Family()
fam.name = "Test10"
fam.accession = "TEST0010"
fam.version = 10
fam.clades = []
fam.consensus = "acgt"
self.assertEqual(
fam.to_fasta(fakedb()),
">Test10\nACGT\n"
)
def test_search_stages(self):
fam = Family()
fam.name = "Test9"
fam.accession = "TEST0009"
fam.version = 9
fam.clades = [2]
fam.consensus = "ACGT"
fam.search_stages = "30,45"
self.assertEqual(
fam.to_fasta(fakedb()),
">Test9 @A_Clade [S:30,45]\nACGT\n"
)
def test_all(self):
fam = Family()
fam.name = "Test7"
fam.accession = "TEST0007"
fam.version = 7
fam.clades = [2, 3]
fam.consensus = "ACGTTGCA" * 20 # 160 bp total
self.assertEqual(
fam.to_fasta(
fakedb(),
use_accession=True,
include_class_in_name=True,
buffer=True,
),
"""\
>TEST0007.7#buffer name=Test7 @A_Clade @Another_Clade_3.
ACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGT
TGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCA
ACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCA
"""
)
self.assertEqual(
fam.to_fasta(
fakedb(),
use_accession=True,
include_class_in_name=True,
do_reverse_complement=True,
buffer=[23, 39],
),
"""\
>TEST0007.7_23_39#buffer (anti) name=Test7 @A_Clade @Another_Clade_3.
GCAACGTTGCAACGTTG
"""
)
def test_multiline(self):
fam = Family()
fam.name = "Test5"
fam.accession = "TEST0005"
fam.version = 5
fam.clades = []
fam.consensus = "ACGTTGCA" * 20 # 160 bp total
self.assertEqual(
fam.to_fasta(fakedb()),
"""\
>Test5
ACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGT
TGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCA
ACGTTGCAACGTTGCAACGTTGCAACGTTGCAACGTTGCA
"""
)
