def test_store_promoters(self):
promoters = [
Promoter("gene1", 10, 20, seq=Seq("cgtacgtacgt")),
Promoter("gene2", 30, 40, seq=Seq("cgtacgtacgt")),
CombinedPromoter("gene3", "gene4", 50, 60, seq=Seq("cgtacgtacgt"))
]
record_with_promoters = create_fake_record()
cassis.store_promoters(
promoters,
record_with_promoters) # add ("store") promoters to seq_record
record_without_promoters = create_fake_record(
) # just the same, without adding promoters
# test promoter features
expected_count = record_without_promoters.get_feature_count() + len(
promoters)
assert expected_count == record_with_promoters.get_feature_count()
for i in range(len(promoters)):
feature = record_with_promoters.get_generics()[i]
assert feature.type == "promoter"
assert feature.get_qualifier("seq") == ("cgtacgtacgt", )
# especially test bidirectional promoter feature (third promoter, last feature)
last_promoter = record_with_promoters.get_generics()[-1]
assert last_promoter.get_qualifier("locus_tag") == ("gene3", "gene4")
assert last_promoter.notes == ["bidirectional promoter"]
def test_regeneration(self):
record = create_fake_record()
results = cassis.CassisResults(record.id)
# create a prediction, since it will generate a border with many extra qualifiers
start_marker = ClusterMarker("gene1", Motif(3, 3, score=1))
start_marker.promoter = "gene1"
start_marker.abundance = 2
end_marker = ClusterMarker("gene4", Motif(3, 3, score=1))
end_marker.promoter = "gene3+gene4"
assert end_marker.abundance == 1
cluster = cassis.ClusterPrediction(start_marker, end_marker)
results.subregions = cassis.create_subregions("gene1", [cluster],
record)
assert results.subregions
results.promoters = [
Promoter("gene1", 10, 20, seq=Seq("cgtacgtacgt")),
Promoter("gene2", 30, 40, seq=Seq("cgtacgtacgt")),
CombinedPromoter("gene3", "gene4", 50, 60, seq=Seq("cgtacgtacgt"))
]
round_trip = cassis.regenerate_previous_results(
results.to_json(), record, None)
assert isinstance(round_trip, cassis.CassisResults)
assert len(results.subregions) == len(round_trip.subregions)
for old, new in zip(results.subregions, round_trip.subregions):
assert old.location == new.location
assert old.to_biopython()[0].qualifiers == new.to_biopython(
)[0].qualifiers
assert round_trip.promoters == results.promoters
def test_get_promoter_sets(self):
meme_dir = os.path.join(self.options.output_dir, "meme")
anchor_promoter = 5
promoters = [
Promoter("gene1", 1, 1, seq=Seq("acgtacgtacgtacgt")),
Promoter("gene2", 2, 2, seq=Seq("acgtacgtacgtacgt")),
CombinedPromoter("gene3",
"gene4",
3,
4,
seq=Seq("acgtacgtacgtacgt")),
Promoter("gene5", 5, 5, seq=Seq("acgtacgtacgtacgt")),
Promoter("gene6", 6, 6, seq=Seq("acgtacgtacgtacgt")),
# promoter with index=5 --> anchor promoter
Promoter("gene7", 7, 7, seq=Seq("acgtacgtacgtacgt")),
Promoter("gene8", 8, 8, seq=Seq("acgtacgtacgtacgt")),
Promoter("gene9", 9, 9, seq=Seq("acgtacgtacgtacgt"))
]
expected_motifs = [
Motif(plus, minus) for plus in range(3)
for minus in range(3 - plus, 6)
]
self.assertEqual(generate_motifs(meme_dir, anchor_promoter, promoters),
expected_motifs)
def test_check_cluster_predictions(self):
seq_record = create_fake_record()
promoters = [
Promoter("gene1", 1, 5),
Promoter("gene2", 6, 10),
CombinedPromoter("gene3", "gene4", 11, 15)
]
ignored_genes = [ # see captured logging
Gene(FeatureLocation(1, 5), locus_tag="gene5")
]
clusters = [
ClusterPrediction(ClusterMarker("gene1", Motif(3, 3, score=1)),
ClusterMarker("gene4", Motif(3, 3, score=1)))
]
expected = [
ClusterPrediction(ClusterMarker("gene1", Motif(3, 3, score=1)),
ClusterMarker("gene4", Motif(3, 3, score=1)))
]
expected[0].start.promoter = "gene1"
expected[0].end.promoter = "gene3+gene4"
expected[0].genes = 4
expected[0].promoters = 3
assert check_cluster_predictions(clusters, seq_record, promoters,
ignored_genes) == expected
def test_get_anchor_promoter(self):
anchor = "gene3"
promoters = [
Promoter("gene1", 1, 1),
Promoter("gene2", 2, 2),
CombinedPromoter("gene3", "gene4", 3, 4),
Promoter("gene5", 5, 5)
]
self.assertEqual(get_anchor_promoter_index(anchor, promoters), 2)
def test_serialisation(self):
for seq in [Seq("ACGT"), "ACGT"]:
for cls, promoter in [(Promoter, Promoter("gene1", 1, 5, seq=seq)),
(CombinedPromoter,
CombinedPromoter("gene1",
"gene2",
2,
7,
seq=seq))]:
round_trip = cls.from_json(promoter.to_json())
assert promoter.seq == round_trip.seq
assert round_trip == promoter
def test_promoter_id(self):
assert Promoter("gene1", 1, 5).get_id() == "gene1"
assert CombinedPromoter("gene1", "gene2", 1,
5).get_id() == "gene1+gene2"