def test_single(self):
"""RdbParser should read single record as (header,seq) tuple"""
res = list(RdbParser(self.oneseq))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, Sequence("AGUCAUCUAGAUHCAUHC"))
self.assertEqual(
first.info,
Info({
"Species": "H.Sapiens",
"OriginalSeq": "AGUCAUCUAGAUHCAUHC"
}),
)
res = list(RdbParser(self.multiline))
self.assertEqual(len(res), 1)
first = res[0]
self.assertEqual(first, Sequence("AGUCAUUAGAUHCAUHC"))
self.assertEqual(
first.info,
Info({
"Species": "H.Sapiens",
"OriginalSeq": "AGUCAUUAGAUHCAUHC"
}),
)
def test_sequence_to_moltype(self):
"""correctly convert to specified moltype"""
s = Sequence("TTTTTTTTTTAAAA", name="test1")
annot1 = s.add_annotation(Feature, "exon", "fred", [(0, 10)])
annot2 = s.add_annotation(Feature, "exon", "trev", [(10, 14)])
got = s.to_moltype("rna")
annot1_slice = str(annot1.get_slice())
annot2_slice = str(annot2.get_slice())
got1_slice = str(got.annotations[0].get_slice())
got2_slice = str(got.annotations[1].get_slice())
self.assertNotEqual(annot1_slice, got1_slice)
self.assertEqual(annot2_slice, got2_slice)
self.assertEqual(got.moltype.label, "rna")
self.assertEqual(got.name, "test1")
s = Sequence("AAGGGGAAAACCCCCAAAAAAAAAATTTTTTTTTTAAA", name="test2")
xx_y = [[[2, 6], 2.4], [[10, 15], 5.1], [[25, 35], 1.3]]
y_valued = s.add_annotation(Variable, "SNP", "freq", xx_y)
got = s.to_moltype("rna")
y_valued_slice = str(y_valued.get_slice())
got_slice = str(str(got.annotations[0].get_slice()))
self.assertNotEqual(y_valued_slice, got_slice)
self.assertEqual(got.moltype.label, "rna")
self.assertEqual(got.name, "test2")
s = Sequence("TTTTTTTTTTAAAAAAAAAA", name="test3")
data = [i for i in range(20)]
annot4 = s.add_annotation(SimpleVariable, "SNP", "freq", data)
got = s.to_moltype(RNA)
annot4_slice = str(annot4.get_slice())
got_slice = str(str(got.annotations[0].get_slice()))
self.assertNotEqual(annot4_slice[:10], got_slice[:10])
self.assertEqual(annot4_slice[10:20], got_slice[10:20])
self.assertEqual(got.moltype.label, "rna")
self.assertEqual(got.name, "test3")
def test_annotable_copy_to_seq(self):
s = Sequence("TTTTTTTTTTAAAA", name="Orig")
annot = s.add_annotation(Feature, "exon", "fred", [(0, 14)])
seq = Sequence("UUUUUUUUUUAAAA", name="Test")
got = annot.copy_to_seq(seq)
self.assertEqual(got._serialisable["parent"], seq)
self.assertEqual(got._serialisable["type"], "exon")
self.assertEqual(got._serialisable["name"], "fred")
with self.assertRaises(AssertionError):
got = annot.copy_to_seq(
Sequence("UUUUUUUUUUUAAAA", name="Wrong_seq"))
def test_init_other_seq(self):
"""Sequence init with other seq should preserve name and info."""
r = self.RNA("UCAGG", name="x", info={"z": 3})
s = Sequence(r)
self.assertEqual(s._seq, "UCAGG")
self.assertEqual(s.name, "x")
self.assertEqual(s.info.z, 3)
def test_copy(self):
"""correctly returns a copy version of self"""
s = Sequence("TTTTTTTTTTAAAA", name="test_copy")
annot1 = s.add_annotation(Feature, "exon", "annot1", [(0, 10)])
annot2 = s.add_annotation(Feature, "exon", "annot2", [(10, 14)])
got = s.copy()
got_annot1 = got.get_annotations_matching(
annotation_type="exon", name="annot1"
)[0]
got_annot2 = got.get_annotations_matching(
annotation_type="exon", name="annot2"
)[0]
self.assertIsNot(got, s)
self.assertIsNot(got_annot1, annot1)
self.assertIsNot(got_annot2, annot2)
self.assertEqual(got.name, s.name)
self.assertEqual(got.info, s.info)
self.assertEqual(got._seq, s._seq)
self.assertEqual(got.moltype, s.moltype)
annot1_slice = str(annot1.get_slice())
annot2_slice = str(annot2.get_slice())
got1_slice = str(got.annotations[0].get_slice())
got2_slice = str(got.annotations[1].get_slice())
self.assertEqual(annot1_slice, got1_slice)
self.assertEqual(annot2_slice, got2_slice)
def test_annotate_from_gff(self):
"""correctly annotates a Sequence from a gff file"""
from cogent3.parse.fasta import FastaParser
fasta_path = os.path.join("data/c_elegans_WS199_dna_shortened.fasta")
gff3_path = os.path.join("data/c_elegans_WS199_shortened_gff.gff3")
name, seq = next(FastaParser(fasta_path))
sequence = Sequence(seq)
sequence.annotate_from_gff(gff3_path)
matches = [m for m in sequence.get_annotations_matching("*", extend_query=True)]
# 13 features with one having 2 parents, so 14 instances should be found
self.assertEqual(len(matches), 14)