def test_metaonly(self):
fam = Family()
fam.name = "Test3"
fam.accession = "TEST0003"
fam.version = 3
fam.clades = [5]
fam.consensus = "ACGTTGCA"
fam.repeat_type = "Test"
fam.repeat_subtype = "Metadata"
self.assertEqual(
fam.to_embl(fakedb(), include_seq=False), """\
ID TEST0003; SV 3; linear; DNA; STD; UNC; 8 BP.
NM Test3
XX
AC TEST0003;
XX
XX
KW Test/Metadata.
XX
OS Species 1
OC Parent Clade; A Clade.
XX
CC
CC RepeatMasker Annotations:
CC Type: Test
CC SubType: Metadata
CC Species: Species_1
CC SearchStages:
CC BufferStages:
XX
//
""")
def test_family():
fam = Family()
fam.accession = "TEST0001"
fam.title = "A Simple Test"
fam.version = 1
fam.clades = [5, 3]
fam.repeat_type = "Type"
fam.repeat_subtype = "SubType"
fam.classification = "root;Type;SubType"
fam.model = """\
HMMER3/f [3.1b2 | February 2015]
NAME TEST0001#Type/SubType
LENG 100
MAXL 122
ALPH DNA
RF yes
MM no
CONS yes
CS no
MAP yes
DATE Mon Aug 17 23:04:43 2015
NSEQ 2000
EFFN 18.549065
CKSUM 765031794
STATS LOCAL MSV -10.5531 0.70202
STATS LOCAL VITERBI -11.4974 0.70202
STATS LOCAL FORWARD -4.5297 0.70202
HMM A C G T
m->m m->i m->d i->m i->i d->m d->d
<snip>
"""
return fam
def test_attached_to_root(self):
fam = Family()
fam.name = "Test6"
fam.accession = "TEST0006"
fam.version = 6
fam.clades = [1]
fam.consensus = "ACGTTGCAGAGACTCT"
fam.repeat_type = "Test"
fam.repeat_subtype = "RootTaxa"
self.assertEqual(
fam.to_embl(fakedb(), include_seq=False), """\
ID TEST0006; SV 6; linear; DNA; STD; UNC; 16 BP.
NM Test6
XX
AC TEST0006;
XX
XX
KW Test/RootTaxa.
XX
XX
CC
CC RepeatMasker Annotations:
CC Type: Test
CC SubType: RootTaxa
CC Species: root
CC SearchStages:
CC BufferStages:
XX
//
""")
def test_simple(self):
fam = Family()
fam.name = "Test1"
fam.accession = "TEST0001"
fam.version = 1
fam.clades = [5]
fam.consensus = "ACGTAAAA"
fam.repeat_type = "Type"
fam.repeat_subtype = "SubType"
self.assertEqual(
fam.to_embl(fakedb()), """\
ID TEST0001; SV 1; linear; DNA; STD; UNC; 8 BP.
NM Test1
XX
AC TEST0001;
XX
XX
KW Type/SubType.
XX
OS Species 1
OC Parent Clade; A Clade.
XX
CC
CC RepeatMasker Annotations:
CC Type: Type
CC SubType: SubType
CC Species: Species_1
CC SearchStages:
CC BufferStages:
XX
SQ Sequence 8 BP; 5 A; 1 C; 1 G; 1 T; 0 other;
acgtaaaa 8
//
""")
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_no_consensus(self):
fam = Family()
fam.name = "Test9"
fam.accession = "TEST0009"
fam.version = 9
fam.clades = [2]
self.assertEqual(fam.to_embl(None), None)
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_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_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_seqonly(self):
fam = Family()
fam.name = "Test4"
fam.accession = "TEST0004"
fam.version = 4
fam.clades = [5]
fam.consensus = "ACGTTGCA"
fam.repeat_type = "Test"
fam.repeat_subtype = "SequenceOnly"
self.assertEqual(
fam.to_embl(fakedb(), include_meta=False), """\
ID TEST0004; SV 4; linear; DNA; STD; UNC; 8 BP.
NM Test4
XX
AC TEST0004;
XX
XX
SQ Sequence 8 BP; 2 A; 2 C; 2 G; 2 T; 0 other;
acgttgca 8
//
""")
def test_multiline(self):
fam = Family()
fam.name = "Test2"
fam.accession = "TEST0002"
fam.version = 2
fam.clades = [5]
fam.consensus = "ACGTTGCA" * 20 # 160 bp total
fam.repeat_type = "Test"
fam.repeat_subtype = "Multiline"
self.assertEqual(
fam.to_embl(fakedb()), """\
ID TEST0002; SV 2; linear; DNA; STD; UNC; 160 BP.
NM Test2
XX
AC TEST0002;
XX
XX
KW Test/Multiline.
XX
OS Species 1
OC Parent Clade; A Clade.
XX
CC
CC RepeatMasker Annotations:
CC Type: Test
CC SubType: Multiline
CC Species: Species_1
CC SearchStages:
CC BufferStages:
XX
SQ Sequence 160 BP; 40 A; 40 C; 40 G; 40 T; 0 other;
acgttgcaac gttgcaacgt tgcaacgttg caacgttgca acgttgcaac gttgcaacgt 60
tgcaacgttg caacgttgca acgttgcaac gttgcaacgt tgcaacgttg caacgttgca 120
acgttgcaac gttgcaacgt tgcaacgttg caacgttgca 160
//
""")
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
"""
)
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_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_cds(self):
fam = Family()
fam.name = "Test8"
fam.accession = "TEST0008"
fam.version = 8
fam.clades = [2]
fam.consensus = "ACGTTGCAGAGACTCT"
fam.repeat_type = "Test"
fam.repeat_subtype = "CodingSequence"
fam.coding_sequences = json.dumps([
{
"cds_start": 1,
"cds_end": 6,
"product": "FAKE",
"exon_count": 1,
"description": "Example coding sequence",
"translation": "TL",
},
{
"cds_start": 5,
"cds_end": 16,
"product": "FAKE2",
"exon_count": 1,
"description": "Another example coding sequence",
"translation": "CRDS",
},
])
self.assertEqual(
fam.to_embl(fakedb(), include_seq=False), """\
ID TEST0008; SV 8; linear; DNA; STD; UNC; 16 BP.
NM Test8
XX
AC TEST0008;
XX
XX
KW Test/CodingSequence.
XX
OS A Clade
OC Parent Clade.
XX
CC
CC RepeatMasker Annotations:
CC Type: Test
CC SubType: CodingSequence
CC Species: A_Clade
CC SearchStages:
CC BufferStages:
XX
FH Key Location/Qualifiers
FH
FT CDS 1..6
FT /product="FAKE"
FT /number=1
FT /note="Example coding sequence"
FT /translation="TL"
FT CDS 5..16
FT /product="FAKE2"
FT /number=1
FT /note="Another example coding sequence"
FT /translation="CRDS"
XX
//
""")
def test_citations(self):
fam = Family()
fam.name = "Test7"
fam.accession = "TEST0007"
fam.version = 7
fam.clades = [2]
fam.consensus = "ACGTTGCAGAGACTCT"
fam.length = 16
fam.repeat_type = "Test"
fam.repeat_subtype = "HasCitations"
fam.citations = json.dumps([
{
"order_added": 1,
"authors": "John Doe",
"title": "Testing Citation Export Formatting",
"journal": "Unit Tests 7(2), 2020.",
},
{
"order_added": 2,
"authors": "Jane Doe",
"title": "Testing Citation Export Formatting",
"journal": "Unit Tests 7(2), 2020.",
},
])
self.assertEqual(
fam.to_embl(fakedb(), include_seq=False), """\
ID TEST0007; SV 7; linear; DNA; STD; UNC; 16 BP.
NM Test7
XX
AC TEST0007;
XX
XX
KW Test/HasCitations.
XX
OS A Clade
OC Parent Clade.
XX
RN [1] (bases 1 to 16)
RA John Doe
RT Testing Citation Export Formatting
RL Unit Tests 7(2), 2020.
XX
RN [2] (bases 1 to 16)
RA Jane Doe
RT Testing Citation Export Formatting
RL Unit Tests 7(2), 2020.
XX
CC
CC RepeatMasker Annotations:
CC Type: Test
CC SubType: HasCitations
CC Species: A_Clade
CC SearchStages:
CC BufferStages:
XX
//
""")
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_special_metadata(self):
fam = Family()
fam.name = "Test5"
fam.accession = "TEST0005"
fam.version = 5
fam.clades = [5, 3]
fam.consensus = "ACGTTGCAGAGAKWCTCT"
fam.repeat_type = "LTR"
fam.repeat_subtype = "BigTest"
fam.aliases = "Repbase:MyLTR1\nOtherDB:MyLTR\n"
fam.refineable = True
self.assertEqual(
fam.to_embl(fakedb()), """\
ID TEST0005; SV 5; linear; DNA; STD; UNC; 18 BP.
NM Test5
XX
AC TEST0005;
XX
XX
DR Repbase; MyLTR1.
XX
KW Long terminal repeat of retrovirus-like element; Test5.
XX
OS Species 1
OC Parent Clade; A Clade.
OS Another Clade (3.)
OC .
XX
CC
CC RepeatMasker Annotations:
CC Type: LTR
CC SubType: BigTest
CC Species: Species_1, Another_Clade_3.
CC SearchStages:
CC BufferStages:
CC Refineable
XX
SQ Sequence 18 BP; 4 A; 4 C; 4 G; 4 T; 2 other;
acgttgcaga gakwctct 18
//
""")
