def test_compound_overlap_reverse(self):
self.feature.location = CompoundLocation([FeatureLocation(15, 24, -1),
FeatureLocation(10, 16, -1)])
assert self.get_sub(0, 1) == FeatureLocation(21, 24, -1)
assert self.get_sub(2, 4) == CompoundLocation([FeatureLocation(15, 18, -1),
FeatureLocation(13, 16, -1)])
assert self.get_sub(4, 5) == FeatureLocation(10, 13, -1)
def test_compound_overlap_forward(self):
self.feature.location = CompoundLocation([FeatureLocation(10, 16, 1),
FeatureLocation(15, 24, 1)])
assert self.get_sub(0, 1) == FeatureLocation(10, 13, 1)
assert self.get_sub(1, 3) == CompoundLocation([FeatureLocation(13, 16, 1),
FeatureLocation(15, 18, 1)])
assert self.get_sub(4, 5) == FeatureLocation(21, 24, 1)
def test_bridging_fails(self):
parts = [
FeatureLocation(9, 12, strand=1),
FeatureLocation(0, 3, strand=1)
]
with self.assertRaisesRegex(ValueError, "bridge the record origin"):
Feature(CompoundLocation(parts, operator="join"),
feature_type="test")
Feature(CompoundLocation(parts[::-1], operator="join"),
feature_type="test")
def test_mixed_strand(self):
bio = self.cds.to_biopython()[0]
for location in [
CompoundLocation([
FeatureLocation(1, 5, strand=-1),
FeatureLocation(8, 10, strand=1)
]),
CompoundLocation([
FeatureLocation(1, 5, strand=1),
FeatureLocation(8, 10, strand=None)
])
]:
bio.location = location
with self.assertRaisesRegex(
ValueError, "compound locations with mixed strands"):
CDSFeature.from_biopython(bio)
def test_compound_reverse(self):
self.feature.location = CompoundLocation([
FeatureLocation(21, 27, -1),
FeatureLocation(12, 15, -1),
FeatureLocation(0, 6, -1)
])
assert self.get_sub(2, 3) == FeatureLocation(12, 15, -1)
def test_extends_past_before(self):
self.reverse_strand()
self.sub_locations[0] = FeatureLocation(BeforePosition(2),
self.sub_locations[0].end,
strand=-1)
self.cds.location = CompoundLocation(self.sub_locations[::-1])
new = self.cds.get_sub_location_from_protein_coordinates(0, 7)
assert new.start == 3
def test_extends_past_after(self):
self.sub_locations[-1] = FeatureLocation(21,
AfterPosition(29),
strand=1)
self.cds.location = CompoundLocation(self.sub_locations)
new = self.cds.get_sub_location_from_protein_coordinates(0, 7)
assert new.end == 27
def test_frameshifted_location(self):
location = CompoundLocation(
[FeatureLocation(3, 9, 1),
FeatureLocation(8, 14, 1)])
assert len(location) == 12
seq = Seq("ATGATGAGCCCTCGTCTAGACTACAATGA")
extracted = location.extract(seq)
assert extracted == "ATGAGCCCCTCG"
assert len(extracted) == len(location)
translation = extracted.translate()
assert translation == "MSPS"
cds = CDSFeature(location, locus_tag="test", translation=translation)
new = cds.get_sub_location_from_protein_coordinates(1, 3)
assert isinstance(new, CompoundLocation)
assert len(new.parts) == 2
assert new.start == 6
assert new.end == 11
def test_compound(self):
location = CompoundLocation(
[FeatureLocation(0, 3),
FeatureLocation(6, 9)])
for good in ["A", "AA"]:
assert _is_valid_translation_length(good, location)
assert not _is_valid_translation_length("AAA", location)
# and with an ambiguous end, that becomes ok
location = CompoundLocation(
[FeatureLocation(0, 3),
FeatureLocation(6, AfterPosition(11))])
assert _is_valid_translation_length("AAA", location)
# and reversed ambiguous end
location = CompoundLocation([
FeatureLocation(BeforePosition(0), 3, -1),
FeatureLocation(6, 9, -1)
])
for good in ["A", "AA", "AAA"]:
assert _is_valid_translation_length(good, location)
def test_compound_reverse(self):
for position_type in self.position_types:
old = CompoundLocation([FeatureLocation(15, position_type(17), -1),
FeatureLocation(5, 12, -1)])
for offset in range(-2, 3):
new = adjust(old, offset)
assert isinstance(new.end, position_type)
assert new.end == old.end + offset
assert new.parts[0].start is old.parts[0].start
for old_part, new_part in zip(old.parts[1:], new.parts[1:]):
assert old_part is new_part
def test_compound_forward(self):
for position_type in self.position_types:
old = CompoundLocation([FeatureLocation(position_type(5), 12, 1),
FeatureLocation(15, 17, 1)])
for offset in range(-2, 3):
new = adjust(old, offset)
assert isinstance(new.start, position_type)
assert new.start == old.start + offset
assert new.parts[0].end is old.parts[0].end
for old_part, new_part in zip(old.parts[1:], new.parts[1:]):
assert old_part is new_part
def reverse_strand(self):
self.magic = self.magic.reverse_complement()
self.magic_split = self.magic_split.reverse_complement()
self.sub_locations = [
FeatureLocation(loc.start, loc.end, strand=loc.strand * -1)
for loc in self.sub_locations
]
self.location = CompoundLocation(
self.sub_locations[::self.sub_locations[0].strand])
self.cds = CDSFeature(self.location,
locus_tag="compound",
translation="A")
def setUp(self):
self.magic_split = Seq("ATGGCAxxxxxxGGTxxxxxxATTTGT")
self.magic = Seq("ATGGCAGGTATTTGT")
self.translation = "MAGIC"
self.sub_locations = [
FeatureLocation(0, 6, strand=1),
FeatureLocation(12, 15, strand=1),
FeatureLocation(21, 27, strand=1)
]
self.location = CompoundLocation(self.sub_locations)
self.cds = CDSFeature(self.location,
locus_tag="compound",
translation="A")
def test_complicated(self):
parts = [
FeatureLocation(121124, 122061, 1),
FeatureLocation(122339, 122383, 1),
FeatureLocation(122559, 122666, 1),
FeatureLocation(122712, 122874, 1),
FeatureLocation(123060, 123337, 1),
FeatureLocation(123481, 123749, 1),
FeatureLocation(123809, 124032, 1),
FeatureLocation(124091, 124193, 1),
FeatureLocation(124236, 124401, 1),
FeatureLocation(124684, 124724, 1)
]
location = CompoundLocation(parts, operator="join")
cds = CDSFeature(location, locus_tag="complicated", translation="A")
seq = (
"ATGAGCCCTCGTCTAGACTACAATGAAGGATACGATTCCGAAGACGAGGAGATCCCCCGTTACGTACACCAT"
"TCTAGAGGAAAGAGTCATAGATCCGTGAGGACGTCAGGTCGCTCACGCACGTTGGATTACGACGGGGATGAT"
"GAAGCTAGTGACCACGCTGCCCCCTCCGGGATTGATCGGGACGCTCGAGCCTGTCCAACATCTCGCAGATAT"
"ACTGATGACTGCCTTGAGACACATAAATTTCGAGGTGCCCGCTCCTCTCGCTCCCGTGGACGAACCGATGAT"
"AACAAGGTTTTGTACTACACCAAGTATCGCAGCCCGGCTAAGGACTTGCCTATCGAGCGTGATCCCGAGGGT"
"ATTAATTTATTCAAGGTCCGACAGCACACACGGCCAAGTGACGCTCATGTGCCCAGTGGATACCGTGAGCCC"
"TACGAAGTCAAGGTCGACGAGTATGAGGATGATCATCCCCGTACATGCACTAGCCGCCGTGACTCTAGACAG"
"CCGAAAGTCTACAAGGTCCGGGTTGATGAGTACGAGGATAACCTCCCTGCACGCTCTCACACTGACTTTCGC"
"GAGTCTCCACGGTCTGAAAGATGCTCTAGCCGCTACACCGAGGACTCGAAGCCTGGGGAGCTTCCTCCCCGC"
"TCAGGGCCCTGTCGGTCCAGCAGGCCTTCTCCGGTCGATGAGGACGTCGAGTATGAGATCCGTGAGCCCCGA"
"GGGCATCGCTCCAGTCGACACTCTACAGATGTTGACTTTCAGCCAGTAGAACAACATCCTCGCTTTGGACAA"
"CGTGGACTCAGCAGACCTTCGCGGGTTGATGAGGAAGTCGATTATGAGATCCGTGAGCCCCGTGGCAATCGT"
"GTCAGTCACGCTGCTCATGGTGACAGCCCCTGTCAGGACCAAAGCTCCAGGCATATCGGCATTCAATTGTGG"
"AGTACGCGCGGACCCCGGGCGGCTGGCCGTGGCCGGGGTCCTGATGAGTCTGACGATGTTGAGCCCTAGGCA"
"GGGAATTGCCGTAATGCTCTTCAAACTGTATAGCAAGCTCAGCATCAATTCTTTAACTGGCAGGCGCTCTGC"
"TCGCGCGTTTCTCTCTTGGGGTGGTTGGTTTGACTGTAGATTTCCTCTTTCAAGGCTTCTAGATACACCTTT"
"GGAAGATAGCAACGCTATGCAAGATATTTTTGATAATTCAAATCCTTTTTACACATGGAATAGCTGGTGTTC"
"CTGTTTTATCTAGGCAATTGACCCACGCCATCTCGGTAGGTACGGTAAAAGCAAGCCGTAATCTCGTATGGC"
"TTCATCCTTAGCATCGTATAGATCTCCACTCGGGACTCGGCCAGGGATCTTCCATCAATCAACGTGAAGAAG"
"TCCAGCACCCCGCTGAATCATAATATCCTACCGATTCTGCTCTCTTCACCTCTAGATACCCCTCTAGACTCC"
"TGTCAACATGTTCCGTACAGTCGAAGACCGCCCGACCCCAAAAGAGGTATATAACTGGCGGCTGTACACCGA"
"GGCCACCATCATTGCCACTGGTACACTCTTGTGAGTAGGTGCTGTTGTAACGAAAAACATCCAACTGATCCG"
"CCAGGTTCGGCTATGACTCGGCTTTTGTGGGAACTACCATTGCCCGCCAAAGCTTCGTTGATGCCTTCAACA"
"TCGTCGAGTCGGAGGCGGCGGATATTTCAAGCAATATCACGTCAACCTTTCAGGCCGGCGCATTTTTCGGCG"
"CCATCTTCTGCTTCTTGCCTGAGTGAAGCCGTTAGAGACGGTCTCACTGGCTAACCGGACCAAGTGACCGAC"
"AAAATTGGGCGTAAATGGGCCCTTCAGGCAAACACACTGCTGTTTCTTATTGGCGCGATTGTGATGACGGCT"
"GCAACACATCACCTTTCCTATATATGTAAGTCATATCCCCGTAGTAGTCAAGGTTGTTAACTAGAGCAGATG"
"CTGGACGAGCTCTCACCGGCATCGCATGCGGCGCTATCACCGCGACCGTCCCCAGCTATATTGCCGAGCTGT"
"CAATCGTGTCGATCCGGGGCTTCCTCACCGGGTTCTTCGAAGTCGCATACCAGATTGGTAGCTTGGTTGGAT"
"TCTGGATCAACTATGGCATTAACGAGAACATGGACAACTCCTCGGCCGCAAGCTGGAGAGTGCCTATGGCAG"
"TCCAGATCATCCCCGCAGGAGTCCTTTTCATTGGTGGCTTTTCCTCCATGAGAGTCCTCTCTGGCTGATGCG"
"AAAAGACAGTGAGGATGCCGCGACGGCTGCCCTGGAGGCGTTGAGGAAACTGCCACGGTCTCATCAATGTAA"
"TCTCCCACCAAGACTCAGGACATAGTCCCATGCTGACTATTTTAGATGTCCAGGAAGACATCGAGATGAACC"
"GCACCAGGCTGCTGGAGGAAGCTCGGATCGCCGAGAAGTACGGACAAGGTTGGTTGGCATATATCCGAGGCG"
"CACTCTTCGAGCTCTCGCGCCATGGGATGTGGAATCGTGTTCTGCTCGTCCTCTGTGCCTTTGCACTGCAGA"
"ATATGTCGGGAGCTGCTGCTATCAACTACTATTCCCCCATACTCTTTGCGTCGTTGGGGATCACTGATGTCG"
"CTCTGTATACAGGTATTTATGGCCTGGTAAAAGGTAAGTTCTTCTCCTTAAGTATCTCTGGCTGACAATAGG"
"GATTAACTGATGAGTTTACAGCCGTCGCATCAATTATATTCTACGGCATTCTCATTGATATGTGGGGCCGCC"
"GACGTCCGACCATTGTTTCGTCACTGGCCTGCCCTCTATGTCTCTGGTTTGTGGGTGCATACGTCAAAGTTG"
"GGCATCCAGCCGATATCATAGACGCCGGCGGGGAATTGTCCCCCTCCACGGAGGCTGGTGGTAGAGCGGCGA"
"CTGCGATGATTATGATCTACTCCGTCTTGTAAGTGCCCCTCACTTTTGAATGGGCTTCAGCTTGGAACTCGA"
"GTAACTGGTATCCAGTTGGTCTTTTGGTCTCAACGGTATCCCCTGGATTGTCTCCGCCGAAATCTTCCCCGG"
"CGCGCTGCGAAATCTCACGGGGACATGGGCTGCGCTGGTGCAATGGTATGCAATTCCCTTCACCTAGTATCC"
"ATATCTAAATCAGCAGGTTGATCCAATTCGTTATCACCAAAGCTCTCCCGTACATCTTCAATAGCCTTGGGT"
"ACGGGACGTGGTTCTTCTTCGCCTCCTGGATGCTGCTCGCTATCATTTGGTCATTCTTTTTTCTCCCGGAAA"
"CCAAGGGGAAGACTCTCGATGAAATGCATACGATCTTGTACGTTTCTCTCCGTCGAAATGTGGTCTTGGCTA"
"ATGAATCAGCGGCCATTCTCTCGCCGAAGAGCAGGGTAAGGGTGAGGTTCGAGATAACACTACTAAAAGTGA"
"TCGGGAGGCTGTCTAGTCCAGTAGTTCTAGAGGACTATTGGCTGGATGATTCCTCTGATGATTTTTGATTGG"
"TGGTGAAAATGTTGGATGTTTAATGCCAATGTACTGGGAGAGAACATGCCGATAGTACATACCGCTGTGTTG"
"TATATCGAAGACGGTTGATTTATATATCTTAGTCTTTCAAAAGACGGCACTCACACAATCACACTTCGATGA"
)
translation = (
"MSPRLDYNEGYDSEDEEIPRYVHHSRGKSHRSVRTSGRSRTLDYDGDDEASDHAAPSGIDRDAR"
"ACPTSRRYTDDCLETHKFRGARSSRSRGRTDDNKVLYYTKYRSPAKDLPIERDPEGINLFKVRQ"
"HTRPSDAHVPSGYREPYEVKVDEYEDDHPRTCTSRRDSRQPKVYKVRVDEYEDNLPARSHTDFR"
"ESPRSERCSSRYTEDSKPGELPPRSGPCRSSRPSPVDEDVEYEIREPRGHRSSRHSTDVDFQPV"
"EQHPRFGQRGLSRPSRVDEEVDYEIREPRGNRVSHAAHGDSPCQDQSSRHIGIQLWTGVPVLSR"
"QLTHAISTPVNMFRTVEDRPTPKEVYNWRLYTEATIIATGTLLFGYDSAFVGTTIARQSFVDAF"
"NIVESEAADISSNITSTFQAGAFFGAIFCFLPEADAGRALTGIACGAITATVPSYIAELSIVSI"
"RGFLTGFFEVAYQIGSLVGFWINYGINENMDNSSAASWRVPMAVQIIPAGVLFIGGFSSMREDI"
"EMNRTRLLEEARIAEKYGQGWLAYIRGALFELSRHGMWNRVLLVLCAFALQNMSGAAAINYYSP"
"ILFASLGITDVALYTGIYGLVKAVASIIFYGILIDMWGRRRPTIVSSLACPLCLWFVGAYVKVG"
"HPADIIDAGGELSPSTEAGGRAATAMIMIYSVFWSFGLNGIPWIVSAEIFPGALRNLTGTWAAL"
"VQWLIQFVITKALPYIFNSLGYGTWFFFASWMLLAIIWSFFFLPETKGKTLDEMHTIFLSKDGT"
"HTITLR")
new = cds.get_sub_location_from_protein_coordinates(353, 412)
# pad the beginning to match the location
assert new.extract(Seq("x" * location.start +
seq)).translate() == translation[353:412]