def create_fake_record():
"""Set up a fake sequence record"""
seq_record = helpers.DummyRecord(
seq=Seq("acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgta" * 196))
seq_record.name = "test"
locations = [
FeatureLocation(100, 300, strand=1),
FeatureLocation(101, 299, strand=-1),
FeatureLocation(250, 350, strand=1),
FeatureLocation(500, 1000, strand=1),
FeatureLocation(1111, 1500, strand=-1),
FeatureLocation(2000, 2200, strand=-1),
FeatureLocation(2999, 4000, strand=1),
FeatureLocation(4321, 5678, strand=1),
FeatureLocation(6660, 9000, strand=-1)
]
for i in range(9):
cds = helpers.DummyCDS(locus_tag="gene" + str(i + 1))
cds.location = locations[i]
seq_record.add_cds_feature(cds)
seq_record.add_gene(
secmet.Gene(locations[i], locus_tag="gene" + str(i + 1)))
if i == 3 or i == 5:
cds.gene_functions.add(secmet.qualifiers.GeneFunction.CORE,
"testtool", "dummy", "product")
return seq_record
def setUp(self):
self.genes = []
self.regions = []
domain_names = self.gen_domain_names()
for product in ['not_atpks', 'transatpks']:
cluster = helpers.DummyProtocluster(1, 2, product=product)
candidate_cluster = helpers.DummyCandidateCluster([cluster])
self.regions.append(Region(candidate_clusters=[candidate_cluster]))
for i in range(7):
locus_tag = chr(ord('a') + i)
if i == 6:
locus_tag = "all"
cds = helpers.DummyCDS(1, 2, locus_tag=locus_tag)
cds.product = product
cds.nrps_pks = DummyNRPSQualfier()
cds.nrps_pks.domain_names = domain_names["nrpspksdomains_" +
locus_tag]
cds.cluster = cluster
cluster.add_cds(cds)
self.genes.append(cds)
self.regions[-1].add_cds(cds)
assert cds.region == self.regions[-1]
self.predictions = [
'redmxmal', 'ccmal', 'ohemal', 'ohmxmal', 'ohmmal', 'ccmmal',
'emal', 'redmmal', 'mmal', 'ccmxmal', 'mxmal', 'redemal', 'ohmal',
'mal', 'ccemal'
]
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
# test gene is AQF52_5530 from CP013129.1
translation = (
"MDTHQREEDPVAARRDRTHYLYLAVIGAVLLGIAVGFLAPGVAVELKPLGTGFVN"
"LIKMMISPIIFCTIVLGVGSVRKAAKVGAVGGLALGYFLVMSTVALAIGLLVGNL"
"LEPGSGLHLTKEIAEAGAKQAEGGGESTPDFLLGIIPTTFVSAFTEGEVLQTLLV"
"ALLAGFALQAMGAAGEPVLRGIGHIQRLVFRILGMIMWVAPVGAFGAIAAVVGAT"
"GAAALKSLAVIMIGFYLTCGLFVFVVLGAVLRLVAGINIWTLLRYLGREFLLILS"
"TSSSESALPRLIAKMEHLGVSKPVVGITVPTGYSFNLDGTAIYLTMASLFVAEAM"
"GDPLSIGEQISLLVFMIIASKGAAGVTGAGLATLAGGLQSHRPELVDGVGLIVGI"
"DRFMSEARALTNFAGNAVATVLVGTWTKEIDKARVTEVLAGNIPFDEKTLVDDHA"
"PVPVPDQRAEGGEEKARAGV")
cds = helpers.DummyCDS(0, len(translation))
cds.translation = translation
results = smcogs.classify("test", [cds], get_config())
assert results.best_hits[cds.get_name(
)].hit_id == "SMCOG1212:sodium:dicarboxylate symporter"
record = helpers.DummyRecord(seq=translation)
record.add_cds_feature(cds)
record.add_protocluster(helpers.DummyProtocluster(0, len(translation)))
# if we don't handle multiple semicolons right, this line will crash
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 setUp(self):
self.genes = []
self.clusters = []
domain_names = self.gen_domain_names()
for product in ['not_atpks', 'transatpks']:
cluster = helpers.DummyCluster(1, 2, products=[product])
assert cluster.products == (product, )
for i in range(7):
locus_tag = chr(ord('a') + i)
if i == 6:
locus_tag = "all"
cds = helpers.DummyCDS(1, 2, locus_tag=locus_tag)
cds.product = product
cds.nrps_pks = DummyNRPSQualfier()
cds.nrps_pks.domain_names = domain_names["nrpspksdomains_" +
locus_tag]
cds.cluster = cluster
cluster.add_cds(cds)
self.genes.append(cds)
self.clusters.append(cluster)
self.predictions = [
'redmxmal', 'ccmal', 'ohemal', 'ohmxmal', 'ohmmal', 'ccmmal',
'emal', 'redmmal', 'mmal', 'ccmxmal', 'mxmal', 'redemal', 'ohmal',
'mal', 'ccemal'
]
def test_cds_removal(self):
record = Record(Seq("A" * 1000))
cluster = helpers.DummyCluster(0, 1000)
record.add_cluster(cluster)
first_cds = helpers.DummyCDS(0, 100, locus_tag="A")
second_cds = helpers.DummyCDS(200, 300, locus_tag="B")
record.add_cds_feature(first_cds)
record.add_cds_feature(second_cds)
assert len(record.get_cds_features()) == 2
assert len(cluster.cds_children) == 2
record.remove_cds_feature(first_cds)
assert len(record.get_cds_features()) == 1
assert len(cluster.cds_children) == 1
assert record.get_cds_features()[0] is list(cluster.cds_children)[0]
assert record.get_cds_features()[0].locus_tag == "B"
def test_cds_cluster_linkage(self):
record = Record("A"*200)
for start, end in [(50, 100), (10, 90), (0, 9), (150, 200)]:
record.add_cds_feature(helpers.DummyCDS(start, end))
for start, end in [(10, 120), (5, 110), (10, 160), (45, 200)]:
record.clear_clusters()
cluster = helpers.DummyCluster(start, end)
record.add_cluster(cluster)
assert len(cluster.cds_children) == 2
for cds in cluster.cds_children:
assert cds.overlaps_with(cluster)
def test_add_when_regenerating(self):
record = helpers.DummyRecord(seq="A"*3800)
record.id = 'Y16952.3.trimmed'
record.add_cds_feature(helpers.DummyCDS(start=0, end=1800, locus_tag="two_domains"))
record.add_cds_feature(helpers.DummyCDS(start=1900, end=4000, locus_tag="one_domain"))
record.add_cds_feature(helpers.DummyCDS(start=4100, end=4400, locus_tag="no_hits"))
two_domain_json = {'domain_hmms': [{'bitscore': 360.7, 'query_end': 428, 'evalue': 2.1e-110, 'hit_id': 'AMP-binding', 'query_start': 35},
{'bitscore': 66.0, 'query_end': 569, 'evalue': 6.3e-21, 'hit_id': 'PCP', 'query_start': 504}],
'motif_hmms': [],
'type': 'NRPS'}
one_domain_json = {'domain_hmms': [{'bitscore': 76.9, 'query_end': 382, 'evalue': 3.9e-24, 'hit_id': 'ECH', 'query_start': 170}],
'motif_hmms': [{'query_start': 18, 'evalue': 4.7e-05, 'query_end': 30, 'bitscore': 16.1, 'hit_id': 'C1_dual_004-017'},
{'query_start': 38, 'evalue': 1.4e-19, 'query_end': 78, 'bitscore': 62.4, 'hit_id': 'C2_DCL_024-062'}],
'type': 'other'}
json = {'cds_results': {'two_domains': two_domain_json,
'one_domain': one_domain_json},
'record_id': record.id,
'schema_version': 1}
assert not record.get_antismash_domains()
assert not record.get_cds_motifs()
results = nrps_pks_domains.domain_identification.NRPSPKSDomains.from_json(json, record)
assert len(results.cds_results) == 2
assert len(record.get_cds_motifs()) == 2
assert len(record.get_antismash_domains()) == 3
two_domains = record.get_cds_by_name("two_domains")
assert two_domains.nrps_pks.type == "NRPS"
assert len(two_domains.nrps_pks.domains) == 2
assert not two_domains.motifs
one_domain = record.get_cds_by_name("one_domain")
assert one_domain.nrps_pks.type == "other"
assert len(one_domain.nrps_pks.domains) == 1
assert len(one_domain.motifs) == 2
no_hits = record.get_cds_by_name("no_hits")
assert not no_hits.nrps_pks
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 = helpers.DummyCDS(locus_tag="test")
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_add_when_regenerating(self):
record = helpers.DummyRecord(seq="A" * 3800)
record.id = 'Y16952.3.trimmed'
record.add_cds_feature(
helpers.DummyCDS(start=0, end=1800, locus_tag="two_domains"))
record.add_cds_feature(
helpers.DummyCDS(start=1900, end=4000, locus_tag="one_domain"))
record.add_cds_feature(
helpers.DummyCDS(start=4100, end=4400, locus_tag="no_hits"))
a_domain = {
'bitscore': 360.7,
'query_end': 428,
'evalue': 2.1e-110,
'hit_id': 'AMP-binding',
'query_start': 35
}
pcp = {
'bitscore': 66.0,
'query_end': 569,
'evalue': 6.3e-21,
'hit_id': 'PCP',
'query_start': 504
}
two_domain_json = {
'domain_hmms': [a_domain, pcp],
'motif_hmms': [],
'modules': [{
"components": [
{
"domain": a_domain
},
{
"domain": pcp
},
]
}],
"ks_subtypes": [],
'type': 'NRPS'
}
one_domain_json = {
'domain_hmms': [{
'bitscore': 76.9,
'query_end': 382,
'evalue': 3.9e-24,
'hit_id': 'ECH',
'query_start': 170
}],
'motif_hmms': [{
'query_start': 18,
'evalue': 4.7e-05,
'query_end': 30,
'bitscore': 16.1,
'hit_id': 'C1_dual_004-017'
}, {
'query_start': 38,
'evalue': 1.4e-19,
'query_end': 78,
'bitscore': 62.4,
'hit_id': 'C2_DCL_024-062'
}],
"modules": [], # arbitrarily none
"ks_subtypes": [],
'type':
'other'
}
json = {
'cds_results': {
'two_domains': two_domain_json,
'one_domain': one_domain_json
},
'record_id':
record.id,
'modules': [],
'schema_version':
nrps_pks_domains.domain_identification.NRPSPKSDomains.
schema_version
}
assert not record.get_antismash_domains()
assert not record.get_cds_motifs()
results = nrps_pks_domains.domain_identification.NRPSPKSDomains.from_json(
json, record)
assert len(results.cds_results) == 2
assert len(record.get_cds_motifs()) == 2
assert len(record.get_antismash_domains()) == 3
assert len(
record.get_antismash_domains_by_tool("nrps_pks_domains")) == 3
two_domains = record.get_cds_by_name("two_domains")
assert two_domains.nrps_pks.type == "NRPS"
assert len(two_domains.nrps_pks.domains) == 2
assert not two_domains.motifs
modules = results.cds_results[two_domains].modules
assert modules
assert modules[0]._loader._domain.hit_id == "AMP-binding"
assert modules[0]._carrier_protein._domain.hit_id == "PCP"
assert not two_domains.modules # added in add_to_record
one_domain = record.get_cds_by_name("one_domain")
assert one_domain.nrps_pks.type == "other"
assert len(one_domain.nrps_pks.domains) == 1
assert len(one_domain.motifs) == 2
assert not results.cds_results[one_domain].modules
assert not one_domain.modules
no_hits = record.get_cds_by_name("no_hits")
assert not no_hits.nrps_pks