def test_other(self):
location = CompoundLocation([FeatureLocation(5922, 6190, strand=1),
FeatureLocation(5741, 5877, strand=1),
FeatureLocation(4952, 5682, strand=1)])
assert self.func(97, 336, location) == (5243, 6064)
location = CompoundLocation([FeatureLocation(5922, 6190, strand=-1),
FeatureLocation(5741, 5877, strand=-1),
FeatureLocation(4952, 5682, strand=-1)])
assert self.func(97, 336, location) == (5078, 5854)
def test_position_conversion_compound_reverse(self):
location = CompoundLocation([FeatureLocation(0, 6, strand=-1),
FeatureLocation(9, 18, strand=-1)])
assert len(location) == 15
assert self.func(0, 4, location) == (3, 18)
assert self.func(1, 5, location) == (0, 15)
location = CompoundLocation([FeatureLocation(0, 6, strand=-1),
FeatureLocation(12, 15, strand=-1),
FeatureLocation(21, 27, strand=-1)])
assert len(location) == 15
assert self.func(0, 4, location) == (3, 27)
assert self.func(1, 5, location) == (0, 24)
assert self.func(2, 3, location) == (12, 15)
def test_position_conversion_nonzero_compound(self):
location = CompoundLocation([FeatureLocation(6, 18, strand=1),
FeatureLocation(24, 27, strand=1)])
assert len(location) == 15
assert self.func(0, 2, location) == (6, 12)
assert self.func(1, 4, location) == (9, 18)
assert self.func(3, 5, location) == (15, 27)
location = CompoundLocation([FeatureLocation(6, 15, strand=-1),
FeatureLocation(21, 27, strand=-1)])
assert len(location) == 15
assert self.func(0, 2, location) == (21, 27)
assert self.func(1, 4, location) == (9, 24)
assert self.func(3, 5, location) == (6, 12)
def test_prepeptide_adjustment(self):
dummy_record = Record(Seq("A"*400, generic_dna))
subregion = DummySubRegion(start=100, end=300)
dummy_record.add_subregion(subregion)
region = Region(subregions=[subregion])
dummy_record.add_region(region)
dummy_prepeptide = DummyFeature(200, 230, 1, "CDS_motif")
# ensure both FeatureLocation and CompoundLocations are handled appropriately
leader_loc = FeatureLocation(200, 210, 1)
tail_loc = CompoundLocation([FeatureLocation(220, 223, -1), FeatureLocation(227, 230, -1)])
dummy_prepeptide._qualifiers["leader_location"] = [str(leader_loc)]
dummy_prepeptide._qualifiers["tail_location"] = [str(tail_loc)]
dummy_record.add_feature(dummy_prepeptide)
# and add a CDS_motif without either qualifier (e.g. NRPS/PKS motif) to ensure that doesn't break
dummy_record.add_feature(DummyFeature(250, 280, 1, "CDS_motif"))
with NamedTemporaryFile(suffix=".gbk") as output:
region.write_to_genbank(output.name)
bio = list(seqio.parse(output.name))[0]
assert len(bio.features) == 4
found = False
for feature in bio.features:
tail = feature.qualifiers.get("tail_location")
leader = feature.qualifiers.get("leader_location")
if tail and leader:
# the part locations should now be adjusted backwards 100 bases
assert leader == ["[100:110](+)"]
assert tail == ["join{[120:123](-), [127:130](-)}"]
found = True
assert found, "prepeptide feature missing in conversion"
def test_single_compound(self):
for strand in [1, -1]:
location = CompoundLocation([
FeatureLocation(6, 9, strand),
FeatureLocation(12, 16, strand)
])
new = build_location_from_others([location])
assert new == location
def setUp(self):
self.seqrec = SeqRecord(UnknownSeq(21))
loc = CompoundLocation([
FeatureLocation(12, 21, strand=1),
FeatureLocation(0, 9, strand=1)
],
operator="join")
self.seqcds = SeqFeature(loc, type="CDS")
self.seqgene = SeqFeature(loc, type="gene")
self.seqrec.annotations["topology"] = "circular"
def test_some_merged(self):
for strand in [1, -1]:
locations = [FeatureLocation(1, 4, strand),
FeatureLocation(6, 9, strand),
FeatureLocation(9, 12, strand),
FeatureLocation(15, 18, strand)]
new = build_location_from_others(locations)
assert isinstance(new, CompoundLocation)
assert new == CompoundLocation([FeatureLocation(1, 4, strand),
FeatureLocation(6, 12, strand),
FeatureLocation(15, 18, strand)])
def setUp(self):
self.seqrec = SeqRecord(Seq("A" * 21))
loc = CompoundLocation([
FeatureLocation(12, 15, strand=1),
FeatureLocation(18, 21, strand=1),
FeatureLocation(0, 3, strand=1),
FeatureLocation(6, 9, strand=1)
],
operator="join")
self.seqcds = SeqFeature(loc, type="CDS")
self.seqgene = SeqFeature(loc, type="gene")
self.seqrec.annotations["topology"] = "circular"
self.seqrec.annotations["molecule_type"] = "DNA"
def test_individual(self):
loc = combine_locations(self.make(3, 7), self.make(5, 9))
assert loc.start == 3 and loc.end == 9
loc = combine_locations(self.make(3, 5), self.make(7, 9))
assert loc.start == 3 and loc.end == 9
loc = combine_locations(self.make(7, 9), self.make(3, 5))
assert loc.start == 3 and loc.end == 9
# it's silly, but since it theoretically is useful for CompoundLocation condensing
loc = combine_locations(self.make(0, 5))
assert loc.start == 0 and loc.end == 5
loc = combine_locations(CompoundLocation([self.make(0, 3), self.make(6, 9)]))
assert loc.start == 0 and loc.end == 9 and len(loc.parts) == 1
def test_compound(self):
first = FeatureLocation(1, 6, strand=1)
second = FeatureLocation(10, 16, strand=1)
location = CompoundLocation([first, second], operator="join")
assert 5 in location
assert 7 not in location
assert 15 in location
new_location = self.convert(location, expected_type=CompoundLocation)
assert location.start == 1
assert 5 in new_location
assert 7 not in new_location
assert 15 in new_location
assert location.end == 16
assert new_location.operator == "join"
def test_compound_location(self):
old = Prepeptide(CompoundLocation(
[FeatureLocation(10, 50, 1),
FeatureLocation(130, 180, 1)],
operator="join"),
peptide_class="test_class",
core="coreseq...",
locus_tag="loc",
tool="test tool",
leader="10chleader",
tail="10chartail")
leader, core, tail = old.to_biopython()
assert leader.location.start == 10
assert leader.location.end == 40
assert isinstance(core.location, CompoundLocation)
assert core.location.start == 40
assert core.location.end == 150
assert tail.location.start == 150
assert tail.location.end == 180
new = Prepeptide.from_biopython(core)
assert str(new.location) == str(old.location)
def build_compound(pairs, strand, operator="join"):
assert len(pairs) >= 2, "invalid CompoundLocation would be created"
parts = []
for start, end in pairs:
parts.append(FeatureLocation(start, end, strand))
return CompoundLocation(parts, operator=operator)
def test_separate(self):
locations = [FeatureLocation(6, 9, 1), FeatureLocation(12, 16, 1)]
new = build_location_from_others(locations)
assert isinstance(new, CompoundLocation)
assert new == CompoundLocation(locations)