def test_cds_function(self):
cds = CDSFeature(FeatureLocation(1, 5, 1), locus_tag="foo")
# default value
assert cds.gene_functions.get_classification() == GeneFunction.OTHER
assert cds.gene_function == GeneFunction.OTHER
# check bad values can't be assigned
with self.assertRaises(AssertionError):
cds.gene_functions.add("other", "a", "b")
with self.assertRaises(AttributeError):
cds.gene_functions = 0
cds.gene_functions.add(GeneFunction.ADDITIONAL, "first_tool", "dummy")
assert cds.gene_functions.get_classification() == GeneFunction.ADDITIONAL
assert cds.gene_function == GeneFunction.ADDITIONAL
# conflicting, so back to OTHER
cds.gene_functions.add(GeneFunction.TRANSPORT, "other_tool", "dummy")
assert cds.gene_functions.get_classification() == GeneFunction.OTHER
assert cds.gene_function == GeneFunction.OTHER
# but smcogs overrides that
cds.gene_functions.add(GeneFunction.REGULATORY, "smcogs", "dummy")
assert cds.gene_functions.get_classification() == GeneFunction.REGULATORY
# and cluster definition overrides even that
cds.gene_functions.add(GeneFunction.CORE, "cluster_definition", "dummy")
assert cds.gene_functions.get_classification() == GeneFunction.CORE
# and that we still have tracked these
smcogs = cds.gene_functions.get_by_tool("smcogs")
assert len(smcogs) == 1
assert smcogs[0].function == GeneFunction.REGULATORY
adds = cds.gene_functions.get_by_function(GeneFunction.ADDITIONAL)
assert len(adds) == 1
assert adds[0].tool == "first_tool"
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")
def test_simple_location_forward_partial(self):
cds = CDSFeature(FeatureLocation(0, 15, 1), locus_tag="simple")
for start, end in [(1, 5), (0, 3), (2, 3), (1, 4)]:
print("testing", start, end)
new = cds.get_sub_location_from_protein_coordinates(start, end)
print(new)
extracted = new.extract(self.magic)
assert extracted == self.magic[start * 3: end * 3]
assert extracted.translate() == self.translation[start:end]
def test_compound_location_reverse_full(self):
self.reverse_strand()
for direction in [1, -1]:
print("sub locations sorted in direction:", direction)
cds = CDSFeature(CompoundLocation(self.sub_locations[::direction]), locus_tag="compound")
new = cds.get_sub_location_from_protein_coordinates(0, 5)
assert isinstance(new, CompoundLocation)
assert len(new.parts) == 3
print(list(map(str, cds.location.parts)))
print(list(map(str, new.parts)))
assert len(new) == len(cds.location)
assert new.extract(self.magic_split).translate() == self.translation[0:5]
def setUp(self):
self.config = build_config([
"--cf-create-clusters", "--cf-mean-threshold", "0.6",
"--cf-min-cds", "5", "--cf-min-pfams", "5"
],
modules=[clusterfinder],
isolated=True)
update_config({"enabled_cluster_types": []})
self.record = DummyRecord(seq=Seq("A" * 2000))
for start, end, probability, pfam_id in [(10, 20, 0.1, 'FAKE007'),
(30, 40, 0.3, 'PF00106'),
(50, 60, 0.4, 'PF00107'),
(60, 70, 0.7, 'PF00109'),
(70, 80, 0.98, 'PF08484'),
(90, 100, 0.8, 'PF02401'),
(100, 110, 0.32, 'PF04369'),
(110, 120, 1.0, 'PF00128'),
(130, 140, 0.2, 'FAKE234'),
(500, 505, None, 'FAKE505'),
(1010, 1020, 0.1, 'FAKE007'),
(1030, 1040, 0.3, 'PF00106'),
(1050, 1060, 0.4, 'PF00107'),
(1060, 1070, 0.7, 'PF00109'),
(1070, 1080, 0.98, 'PF08484'),
(1090, 1100, 0.8, 'PF02401'),
(1100, 1110, 0.32, 'PF04369'),
(1110, 1120, 1.0, 'PF00128')]:
location = FeatureLocation(start, end)
self.record.add_cds_feature(
CDSFeature(location, locus_tag=str(start)))
pfam = PFAMDomain(location, "dummy_description")
pfam.db_xref.append(pfam_id)
pfam.probability = probability
self.record.add_pfam_domain(pfam)
def test_compound_location_reverse_multiple(self):
self.reverse_strand()
for direction in [1, -1]:
print("sub locations sorted in direction:", direction)
cds = CDSFeature(CompoundLocation(self.sub_locations[::direction]), locus_tag="compound")
new = cds.get_sub_location_from_protein_coordinates(2, 4)
assert isinstance(new, CompoundLocation)
print(list(map(str, cds.location.parts)))
print(list(map(str, new.parts)))
assert len(new.parts) == 2
assert len(new) == 6
assert new.parts[0].start == 12
assert new.parts[0].end == 15
assert new.parts[1].start == 3
assert new.parts[1].end == 6
assert new.extract(self.magic_split).translate() == self.translation[2:4]
def test_classification_with_colon(self):
# since SMCOG id and description are stored in a string separated by :,
# ensure that descriptions containing : are properly handled
cds = CDSFeature(FeatureLocation(0, 100),
locus_tag="test",
translation="AAA")
record = helpers.DummyRecord(features=[cds], seq="A" * 100)
record.add_cluster(helpers.DummyCluster(0, 100))
results = SMCOGResults(record.id)
results.best_hits[cds.get_name()] = HMMResult(
"SMCOG1212:sodium:dicarboxylate_symporter", 0, 100, 2.3e-126, 416)
results.add_to_record(record)
gene_functions = cds.gene_functions.get_by_tool("smcogs")
assert len(gene_functions) == 1
assert str(gene_functions[0]).startswith(
"transport (smcogs) SMCOG1212:sodium:dicarboxylate_symporter"
" (Score: 416; E-value: 2.3e-126)")
def test_compound_location_reverse_single(self):
self.reverse_strand()
for direction in [1, -1]:
print("sub locations sorted in direction:", direction)
cds = CDSFeature(CompoundLocation(self.sub_locations[::direction]), locus_tag="compound")
new = cds.get_sub_location_from_protein_coordinates(0, 2)
assert isinstance(new, FeatureLocation)
assert len(new) == 6
assert new.start == 21
assert new.end == 27
assert new.extract(self.magic_split).translate() == self.translation[0:2]
new = cds.get_sub_location_from_protein_coordinates(2, 3)
assert isinstance(new, FeatureLocation)
assert len(new) == 3
assert new.start == 12
assert new.end == 15
assert new.extract(self.magic_split).translate() == self.translation[2:3]
def test_cds_function_conversion(self):
cds = CDSFeature(FeatureLocation(1, 5, 1), locus_tag="foo")
assert cds.gene_function == GeneFunction.OTHER
assert CDSFeature.from_biopython(cds.to_biopython()[0]).gene_function == GeneFunction.OTHER
cds.gene_functions.add(GeneFunction.ADDITIONAL, "tool", "desc")
assert cds.gene_function == GeneFunction.ADDITIONAL
assert CDSFeature.from_biopython(cds.to_biopython()[0]).gene_function == GeneFunction.ADDITIONAL
def test_membership(self):
location = FeatureLocation(0, 1, strand=1)
# Features don't have locus tags
with self.assertRaises(AttributeError):
Feature(location, feature_type="none").locus_tag = "something"
# CDSFeatures don't have an 'other_value'
with self.assertRaises(AttributeError):
CDSFeature(location, translation="none", gene="a").other_value = 1
cluster = Cluster(location, 0, 0, products=["a", "b"])
assert cluster.products == ("a", "b")
# Clusters have products, not product
with self.assertRaises(AttributeError):
cluster.product = ["c", "d"]
def generate_motif_features(record: Record, feature: CDSFeature,
motifs: List[HMMResult]) -> List[CDSMotif]:
""" Convert a list of HMMResult to a list of CDSMotif features """
# use a locus tag if one exists
locus_tag = feature.get_name()
if feature.locus_tag:
locus_tag = feature.locus_tag
# grab the translation table if it's there
if feature.transl_table:
transl_table = feature.transl_table
else:
transl_table = 1
motif_features = []
for i, motif in enumerate(motifs):
i += 1 # user facing, so 1-indexed
loc = feature.get_sub_location_from_protein_coordinates(
motif.query_start, motif.query_end)
new_motif = CDSMotif(loc)
new_motif.label = motif.hit_id
new_motif.motif = motif.hit_id # TODO: why both label AND motif?
new_motif.domain_id = 'nrpspksmotif_{}_{:04d}'.format(locus_tag, i)
new_motif.evalue = motif.evalue
new_motif.score = motif.bitscore
new_motif.tool = "pksnrpsmotif"
new_motif.detection = "hmmscan"
new_motif.database = "abmotifs"
new_motif.locus_tag = locus_tag
new_motif.translation = str(
new_motif.extract(record.seq).translate(table=transl_table))
new_motif.notes.append(
"NRPS/PKS Motif: %s (e-value: %s, bit-score: %s)" %
(motif.hit_id, motif.evalue,
motif.bitscore)) # TODO move to CDSMotif
motif_features.append(new_motif)
return motif_features
def test_required_identifiers(self):
with self.assertRaises(ValueError):
CDSFeature(FeatureLocation(1, 5, 1))
assert CDSFeature(FeatureLocation(1, 5, 1), locus_tag="foo")
assert CDSFeature(FeatureLocation(1, 5, 1), protein_id="foo")
assert CDSFeature(FeatureLocation(1, 5, 1), gene="foo")
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")
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]
def generate_domain_features(
record: Record, gene: CDSFeature,
domains: List[HMMResult]) -> Dict[HMMResult, AntismashDomain]:
""" Generates AntismashDomain features for each provided HMMResult
Arguments:
record: the record the new features will belong to
gene: the CDSFeature the domains were found in
domains: a list of HMMResults found in the CDSFeature
Returns:
a dictionary mapping the HMMResult used to the matching AntismashDomain
"""
new_features = {}
nrat = 0
nra = 0
nrcal = 0
nrkr = 0
nrXdom = 0
for domain in domains:
loc = gene.get_sub_location_from_protein_coordinates(
domain.query_start, domain.query_end)
# set up new feature
new_feature = AntismashDomain(loc)
new_feature.domain = domain.hit_id
new_feature.locus_tag = gene.locus_tag
new_feature.detection = "hmmscan"
new_feature.database = "nrpspksdomains.hmm"
new_feature.evalue = domain.evalue
new_feature.score = domain.bitscore
transl_table = gene.transl_table or 1
new_feature.translation = str(
new_feature.extract(record.seq).translate(table=transl_table))
if domain.hit_id == "AMP-binding":
nra += 1
domainname = "{}_A{}".format(gene.get_name(), nra)
new_feature.label = domainname
new_feature.domain_id = "nrpspksdomains_" + domainname
elif domain.hit_id == "PKS_AT":
nrat += 1
domainname = "{}_AT{}".format(gene.get_name(), nrat)
new_feature.label = domainname
new_feature.domain_id = "nrpspksdomains_" + domainname
elif domain.hit_id == "CAL_domain":
nrcal += 1
domainname = gene.get_name() + "_CAL" + str(nrcal)
new_feature.label = domainname
new_feature.domain_id = "nrpspksdomains_" + domainname
elif domain.hit_id == "PKS_KR":
nrkr += 1
domainname = gene.get_name() + "_KR" + str(nrkr)
new_feature.label = domainname
new_feature.domain_id = "nrpspksdomains_" + domainname
else:
nrXdom += 1
new_feature.domain_id = "nrpspksdomains_" + gene.get_name(
).partition(".")[0] + "_Xdom" + '{:02d}'.format(nrXdom)
assert new_feature.get_name() not in new_features
new_features[domain] = new_feature
return new_features
def test_simple_location_forward_complete(self):
cds = CDSFeature(FeatureLocation(0, 15, 1), locus_tag="simple")
new = cds.get_sub_location_from_protein_coordinates(0, 5)
extracted = new.extract(self.magic)
assert extracted == self.magic
assert extracted.translate() == self.translation
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=-1) for loc in self.sub_locations]
self.location = CompoundLocation(self.sub_locations)
self.cds = CDSFeature(self.location, locus_tag="compound")
def create_cds(self, start, end, strand=1):
return CDSFeature(FeatureLocation(start, end, strand),
locus_tag="%d-%d" % (start, end))
class TestCDSProteinLocation(unittest.TestCase):
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")
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=-1) for loc in self.sub_locations]
self.location = CompoundLocation(self.sub_locations)
self.cds = CDSFeature(self.location, locus_tag="compound")
def test_simple_location_forward_complete(self):
cds = CDSFeature(FeatureLocation(0, 15, 1), locus_tag="simple")
new = cds.get_sub_location_from_protein_coordinates(0, 5)
extracted = new.extract(self.magic)
assert extracted == self.magic
assert extracted.translate() == self.translation
def test_simple_location_forward_partial(self):
cds = CDSFeature(FeatureLocation(0, 15, 1), locus_tag="simple")
for start, end in [(1, 5), (0, 3), (2, 3), (1, 4)]:
print("testing", start, end)
new = cds.get_sub_location_from_protein_coordinates(start, end)
print(new)
extracted = new.extract(self.magic)
assert extracted == self.magic[start * 3: end * 3]
assert extracted.translate() == self.translation[start:end]
def test_compound_location_forward_full(self):
new = self.cds.get_sub_location_from_protein_coordinates(0, 5)
assert isinstance(new, CompoundLocation)
assert len(new.parts) == 3
print(list(map(str, self.cds.location.parts)))
print(list(map(str, new.parts)))
assert len(new) == len(self.cds.location)
assert new == self.location, "%s != %s" % (str(new), str(self.location))
extracted = new.extract(self.magic_split)
assert extracted == self.magic
assert extracted.translate() == self.translation[0:5]
def test_compound_forward_within_single(self):
new = self.cds.get_sub_location_from_protein_coordinates(0, 2)
assert isinstance(new, FeatureLocation)
assert len(new) == 6
assert new.start == 0
assert new.end == 6
assert new.extract(self.magic_split).translate() == self.translation[0:2]
new = self.cds.get_sub_location_from_protein_coordinates(2, 3)
assert isinstance(new, FeatureLocation)
assert len(new) == 3
assert new.start == 12
assert new.end == 15
assert new.extract(self.magic_split).translate() == self.translation[2:3]
def test_compound_forward_over_multiple(self):
new = self.cds.get_sub_location_from_protein_coordinates(2, 4)
assert isinstance(new, CompoundLocation)
print(list(map(str, self.cds.location.parts)))
print(list(map(str, new.parts)))
assert len(new.parts) == 2
assert len(new) == 6
assert new.parts[0].start == 12
assert new.parts[0].end == 15
assert new.parts[1].start == 21
assert new.parts[1].end == 24
assert new.extract(self.magic_split).translate() == self.translation[2:4]
def test_compound_location_reverse_full(self):
self.reverse_strand()
for direction in [1, -1]:
print("sub locations sorted in direction:", direction)
cds = CDSFeature(CompoundLocation(self.sub_locations[::direction]), locus_tag="compound")
new = cds.get_sub_location_from_protein_coordinates(0, 5)
assert isinstance(new, CompoundLocation)
assert len(new.parts) == 3
print(list(map(str, cds.location.parts)))
print(list(map(str, new.parts)))
assert len(new) == len(cds.location)
assert new.extract(self.magic_split).translate() == self.translation[0:5]
def test_compound_location_reverse_single(self):
self.reverse_strand()
for direction in [1, -1]:
print("sub locations sorted in direction:", direction)
cds = CDSFeature(CompoundLocation(self.sub_locations[::direction]), locus_tag="compound")
new = cds.get_sub_location_from_protein_coordinates(0, 2)
assert isinstance(new, FeatureLocation)
assert len(new) == 6
assert new.start == 21
assert new.end == 27
assert new.extract(self.magic_split).translate() == self.translation[0:2]
new = cds.get_sub_location_from_protein_coordinates(2, 3)
assert isinstance(new, FeatureLocation)
assert len(new) == 3
assert new.start == 12
assert new.end == 15
assert new.extract(self.magic_split).translate() == self.translation[2:3]
def test_compound_location_reverse_multiple(self):
self.reverse_strand()
for direction in [1, -1]:
print("sub locations sorted in direction:", direction)
cds = CDSFeature(CompoundLocation(self.sub_locations[::direction]), locus_tag="compound")
new = cds.get_sub_location_from_protein_coordinates(2, 4)
assert isinstance(new, CompoundLocation)
print(list(map(str, cds.location.parts)))
print(list(map(str, new.parts)))
assert len(new.parts) == 2
assert len(new) == 6
assert new.parts[0].start == 12
assert new.parts[0].end == 15
assert new.parts[1].start == 3
assert new.parts[1].end == 6
assert new.extract(self.magic_split).translate() == self.translation[2:4]
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")
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]