def generate_motif_features(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
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)
prot_loc = FeatureLocation(motif.query_start, motif.query_end)
new_motif = CDSMotif(loc,
feature.get_name(),
prot_loc,
tool="nrps_pks_domains")
new_motif.label = motif.hit_id
new_motif.domain_id = 'nrpspksmotif_{}_{:04d}'.format(locus_tag, i)
new_motif.evalue = motif.evalue
new_motif.score = motif.bitscore
new_motif.detection = "hmmscan"
new_motif.database = "abmotifs"
new_motif.locus_tag = locus_tag
new_motif.translation = feature.translation[motif.query_start:motif.
query_end]
motif_features.append(new_motif)
return motif_features
def generate_domain_features(gene: CDSFeature, domains: List[HMMResult]) -> Dict[HMMResult, AntismashDomain]:
""" Generates AntismashDomain features for each provided HMMResult
Arguments:
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 = {}
domain_counts = defaultdict(int) # type: Dict[str, int]
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, tool="nrps_pks_domains")
new_feature.domain = domain.hit_id
new_feature.locus_tag = gene.locus_tag or gene.get_name()
new_feature.detection = "hmmscan"
new_feature.database = "nrpspksdomains.hmm"
new_feature.evalue = domain.evalue
new_feature.score = domain.bitscore
new_feature.translation = gene.translation[domain.query_start:domain.query_end + 1]
domain_counts[domain.hit_id] += 1 # 1-indexed, so increment before use
domain_name = "{}_{}.{}".format(gene.get_name(), domain.hit_id, domain_counts[domain.hit_id])
new_feature.domain_id = "nrpspksdomains_" + domain_name
new_feature.label = domain_name
new_features[domain] = new_feature
return new_features
def test_simple_location_forward_complete(self):
cds = CDSFeature(FeatureLocation(0, 15, 1),
locus_tag="simple",
translation="A")
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_invalid_qualifier(self):
cds = CDSFeature(FeatureLocation(1, 5, 1),
locus_tag="test",
translation="A")
for bad in ["bad", ["stuff"], {}, 1]:
with self.assertRaisesRegex(
TypeError,
"can only be set to an instance of SecMetQualifier"):
cds.sec_met = bad
def test_simple_location_forward_partial(self):
cds = CDSFeature(FeatureLocation(0, 15, 1),
locus_tag="simple",
translation="A")
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_translation_outside_record(self):
rec = DummyRecord(seq="A" * 10)
for location in [
FeatureLocation(0, AfterPosition(6), strand=1),
FeatureLocation(BeforePosition(4), 10, strand=-1)
]:
bio = SeqFeature(location, type="CDS")
bio.qualifiers["translation"] = ["M" * 5]
with self.assertRaisesRegex(SecmetInvalidInputError,
"translation extends out of record"):
CDSFeature.from_biopython(bio, record=rec)
def test_compound_location_reverse_full(self):
self.reverse_strand()
cds = CDSFeature(self.location, locus_tag="compound", translation="A")
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 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_required_identifiers(self):
with self.assertRaisesRegex(
ValueError,
"requires at least one of: gene, protein_id, locus_tag"):
CDSFeature(FeatureLocation(1, 5, 1), translation="A")
assert CDSFeature(FeatureLocation(1, 5, 1),
locus_tag="foo",
translation="A")
assert CDSFeature(FeatureLocation(1, 5, 1),
protein_id="foo",
translation="A")
assert CDSFeature(FeatureLocation(1, 5, 1),
gene="foo",
translation="A")
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, 'PF77777'),
(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, 'PF77776'),
(500, 505, None, 'PF77775'),
(1010, 1020, 0.1, 'PF77774'),
(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, strand=1)
self.record.add_cds_feature(CDSFeature(location, locus_tag=str(start), translation="A"))
pfam = PFAMDomain(location, "dummy_description", protein_start=start + 1,
protein_end=end-1, identifier=pfam_id, tool="test")
pfam.domain_id = "pfam_%d" % start
pfam.probability = probability
self.record.add_pfam_domain(pfam)
def test_without_genefunctions(self):
bio = self.convert()
assert "gene_functions" not in bio.qualifiers
assert "gene_kind" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.gene_functions
def test_compound_location_reverse_multiple(self):
self.reverse_strand()
cds = CDSFeature(self.location, locus_tag="compound", translation="A")
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_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_bad_translation(self):
loc = FeatureLocation(1, 5, 1)
for trans in [None, "A?", "A!", ""]:
with self.assertRaisesRegex(
ValueError,
"valid translation required|invalid translation characters"
):
CDSFeature(loc, locus_tag="test", translation=trans)
def test_without_secmet(self):
assert not self.cds.sec_met
bio = self.convert()
assert "sec_met" not in bio.qualifiers # for detecting legacy versions
assert "sec_met_domain" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.sec_met
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_location_reverse_single(self):
self.reverse_strand()
cds = CDSFeature(self.location, locus_tag="compound", translation="A")
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_with_genefunctions(self):
self.cds.gene_functions.add(GeneFunction.ADDITIONAL, "testtool",
"dummy")
bio = self.convert()
assert "gene_functions" in bio.qualifiers
assert bio.qualifiers["gene_kind"] == [str(
self.cds.gene_function)] == ["biosynthetic-additional"]
regen = CDSFeature.from_biopython(bio)
assert regen.gene_function == self.cds.gene_function
assert regen.gene_functions.get_by_tool(
"testtool") == self.cds.gene_functions.get_by_tool("testtool")
def test_basics(self):
bio = self.convert()
assert bio.location == self.cds.location
assert bio.qualifiers["locus_tag"] == ["loctag"]
assert bio.qualifiers["gene"] == ["gene"]
assert bio.qualifiers["protein_id"] == ["prot_id"]
assert bio.qualifiers["translation"] == ["A" * 4]
regen = CDSFeature.from_biopython(bio)
assert regen.location == self.cds.location
assert regen.locus_tag == self.cds.locus_tag
assert regen.gene == self.cds.gene
assert regen.protein_id == self.cds.protein_id
def test_with_secmet(self):
domains = [
SecMetQualifier.Domain("testA", 0.1, 1.1, 3, "test"),
SecMetQualifier.Domain("testB", 5.1, 3.9, 5, "dummy")
]
self.cds.sec_met = SecMetQualifier(domains)
bio = self.convert()
assert "sec_met" not in bio.qualifiers # again, detecting leftover legacy versions
assert len(bio.qualifiers["sec_met_domain"]) == 2
assert bio.qualifiers["sec_met_domain"] == list(map(str, domains))
regen = CDSFeature.from_biopython(bio)
assert regen.sec_met
assert len(regen.sec_met.domains) == len(domains)
assert regen.sec_met.domains == domains
def setUp(self):
self.cds = CDSFeature(FeatureLocation(0, 12, 1),
translation="A" * 4,
locus_tag="loctag",
gene="gene",
protein_id="prot_id")
class TestCDSBiopythonConversion(unittest.TestCase):
def setUp(self):
self.cds = CDSFeature(FeatureLocation(0, 12, 1),
translation="A" * 4,
locus_tag="loctag",
gene="gene",
protein_id="prot_id")
def convert(self):
bio_features = self.cds.to_biopython()
assert isinstance(bio_features, list)
assert len(bio_features) == 1
return bio_features[0]
def test_basics(self):
bio = self.convert()
assert bio.location == self.cds.location
assert bio.qualifiers["locus_tag"] == ["loctag"]
assert bio.qualifiers["gene"] == ["gene"]
assert bio.qualifiers["protein_id"] == ["prot_id"]
assert bio.qualifiers["translation"] == ["A" * 4]
regen = CDSFeature.from_biopython(bio)
assert regen.location == self.cds.location
assert regen.locus_tag == self.cds.locus_tag
assert regen.gene == self.cds.gene
assert regen.protein_id == self.cds.protein_id
def test_without_genefunctions(self):
bio = self.convert()
assert "gene_functions" not in bio.qualifiers
assert "gene_kind" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.gene_functions
def test_with_genefunctions(self):
self.cds.gene_functions.add(GeneFunction.ADDITIONAL, "testtool",
"dummy")
bio = self.convert()
assert "gene_functions" in bio.qualifiers
assert bio.qualifiers["gene_kind"] == [str(
self.cds.gene_function)] == ["biosynthetic-additional"]
regen = CDSFeature.from_biopython(bio)
assert regen.gene_function == self.cds.gene_function
assert regen.gene_functions.get_by_tool(
"testtool") == self.cds.gene_functions.get_by_tool("testtool")
def test_without_secmet(self):
assert not self.cds.sec_met
bio = self.convert()
assert "sec_met" not in bio.qualifiers # for detecting legacy versions
assert "sec_met_domain" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.sec_met
def test_with_secmet(self):
domains = [
SecMetQualifier.Domain("testA", 0.1, 1.1, 3, "test"),
SecMetQualifier.Domain("testB", 5.1, 3.9, 5, "dummy")
]
self.cds.sec_met = SecMetQualifier(domains)
bio = self.convert()
assert "sec_met" not in bio.qualifiers # again, detecting leftover legacy versions
assert len(bio.qualifiers["sec_met_domain"]) == 2
assert bio.qualifiers["sec_met_domain"] == list(map(str, domains))
regen = CDSFeature.from_biopython(bio)
assert regen.sec_met
assert len(regen.sec_met.domains) == len(domains)
assert regen.sec_met.domains == domains
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)
class TestCDSBiopythonConversion(unittest.TestCase):
def setUp(self):
self.cds = CDSFeature(FeatureLocation(0, 12, 1),
translation="A" * 4,
locus_tag="loctag",
gene="gene",
protein_id="prot_id")
def convert(self):
bio_features = self.cds.to_biopython()
assert isinstance(bio_features, list)
assert len(bio_features) == 1
return bio_features[0]
def test_basics(self):
bio = self.convert()
assert bio.location == self.cds.location
assert bio.qualifiers["locus_tag"] == ["loctag"]
assert bio.qualifiers["gene"] == ["gene"]
assert bio.qualifiers["protein_id"] == ["prot_id"]
assert bio.qualifiers["translation"] == ["A" * 4]
regen = CDSFeature.from_biopython(bio)
assert regen.location == self.cds.location
assert regen.locus_tag == self.cds.locus_tag
assert regen.gene == self.cds.gene
assert regen.protein_id == self.cds.protein_id
def test_without_genefunctions(self):
bio = self.convert()
assert "gene_functions" not in bio.qualifiers
assert "gene_kind" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.gene_functions
def test_with_genefunctions(self):
self.cds.gene_functions.add(GeneFunction.ADDITIONAL, "testtool",
"dummy")
bio = self.convert()
assert "gene_functions" in bio.qualifiers
assert bio.qualifiers["gene_kind"] == [str(
self.cds.gene_function)] == ["biosynthetic-additional"]
regen = CDSFeature.from_biopython(bio)
assert regen.gene_function == self.cds.gene_function
assert regen.gene_functions.get_by_tool(
"testtool") == self.cds.gene_functions.get_by_tool("testtool")
def test_without_secmet(self):
assert not self.cds.sec_met
bio = self.convert()
assert "sec_met" not in bio.qualifiers # for detecting legacy versions
assert "sec_met_domain" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.sec_met
def test_with_secmet(self):
domains = [
SecMetQualifier.Domain("testA", 0.1, 1.1, 3, "test"),
SecMetQualifier.Domain("testB", 5.1, 3.9, 5, "dummy")
]
self.cds.sec_met = SecMetQualifier(domains)
bio = self.convert()
assert "sec_met" not in bio.qualifiers # again, detecting leftover legacy versions
assert len(bio.qualifiers["sec_met_domain"]) == 2
assert bio.qualifiers["sec_met_domain"] == list(map(str, domains))
regen = CDSFeature.from_biopython(bio)
assert regen.sec_met
assert len(regen.sec_met.domains) == len(domains)
assert regen.sec_met.domains == domains
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)
# compound locations starting with an invalid strand will be treated as per a non-compound wtih a bad strand
def test_translation_outside_record(self):
rec = DummyRecord(seq="A" * 10)
for location in [
FeatureLocation(0, AfterPosition(6), strand=1),
FeatureLocation(BeforePosition(4), 10, strand=-1)
]:
bio = SeqFeature(location, type="CDS")
bio.qualifiers["translation"] = ["M" * 5]
with self.assertRaisesRegex(SecmetInvalidInputError,
"translation extends out of record"):
CDSFeature.from_biopython(bio, record=rec)
def test_invalid_translation_table(self):
bio = self.cds.to_biopython()[0]
bio.qualifiers["transl_table"] = ["11a"]
with self.assertRaisesRegex(SecmetInvalidInputError,
"invalid translation table"):
CDSFeature.from_biopython(bio)
def test_bad_strand(self):
with self.assertRaisesRegex(ValueError, "Strand must be"):
CDSFeature(FeatureLocation(1, 5, 0),
locus_tag="test",
translation="A")
def test_bad_strand(self):
for strand in [0, None]:
with self.assertRaisesRegex(ValueError, "invalid strand"):
CDSFeature(FeatureLocation(1, 5, strand),
locus_tag="test",
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]
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",
translation="A")
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 test_simple_location_forward_complete(self):
cds = CDSFeature(FeatureLocation(0, 15, 1),
locus_tag="simple",
translation="A")
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",
translation="A")
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()
cds = CDSFeature(self.location, locus_tag="compound", translation="A")
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()
cds = CDSFeature(self.location, locus_tag="compound", translation="A")
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()
cds = CDSFeature(self.location, locus_tag="compound", translation="A")
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_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_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]
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_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_invalid_translation_table(self):
bio = self.cds.to_biopython()[0]
bio.qualifiers["transl_table"] = ["11a"]
with self.assertRaisesRegex(SecmetInvalidInputError,
"invalid translation table"):
CDSFeature.from_biopython(bio)
def __init__(self, feature: CDSFeature) -> None:
super().__init__(["id", "sequence", "domains", "modules"])
self.sequence = feature.translation
self.id = feature.get_name()
self.domains = [] # type: List[JSONDomain]
self.modules = [] # type: List[JSONModule]
