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test_transform.py
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test_transform.py
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#To run these tests, run "pytest" from the command line
from VCI2DMWG import *
from interpretation_generated import *
import json
class MockNode(Node):
def add_contribution(self,c):
self.contribution = c
class CodingUsingNode(Node):
def __init__(self,iri=None):
self.data = None
@get_factory_coding('VS003')
def add_value(self,x):
self.data = x
class ConceptUsingNode(Node):
def __init__(self,iri=None):
self.data = None
@get_factory_concept('VS003')
def add_value(self,x):
self.data = x
#Add a coding, it should pass directly through
def test_add_coding_directly():
node=CodingUsingNode()
c = Coding()
node.add_value(c)
assert node.data == c
#Add a string, it should find the right coding
def test_add_coding_by_code():
node=CodingUsingNode()
node.add_value('LA6668-3')
coding = node.data
assert isinstance(coding, Coding)
assert coding.get_id() == 'http://loinc.org/LA6668-3'
assert coding.get_code() == 'LA6668-3'
assert coding.get_system() == 'http://loinc.org/'
assert coding.get_display() == 'Pathogenic'
def test_add_coding_by_id():
node=CodingUsingNode()
node.add_value('http://loinc.org/LA6668-3')
coding = node.data
assert isinstance(coding, Coding)
assert coding.get_id() == 'http://loinc.org/LA6668-3'
assert coding.get_code() == 'LA6668-3'
assert coding.get_system() == 'http://loinc.org/'
assert coding.get_display() == 'Pathogenic'
def test_add_coding_by_display():
node=CodingUsingNode()
node.add_value('Pathogenic')
coding = node.data
assert isinstance(coding, Coding)
assert coding.get_id() == 'http://loinc.org/LA6668-3'
assert coding.get_code() == 'LA6668-3'
assert coding.get_system() == 'http://loinc.org/'
assert coding.get_display() == 'Pathogenic'
def test_add_coding_not_found():
node=CodingUsingNode()
caught=False
try:
node.add_value('derp')
except:
caught = True
assert caught
def test_add_concept_directly():
node=ConceptUsingNode()
cc = CodeableConcept()
node.add_value(cc)
concept = node.data
assert concept == cc
def test_add_concept_by_code():
node=ConceptUsingNode()
node.add_value('LA6668-3')
concept = node.data
coding = concept.get_coding()[0]
assert isinstance(coding, Coding)
assert coding.get_id() == 'http://loinc.org/LA6668-3'
assert coding.get_code() == 'LA6668-3'
assert coding.get_system() == 'http://loinc.org/'
assert coding.get_display() == 'Pathogenic'
def test_add_concept_by_id():
node=ConceptUsingNode()
node.add_value('http://loinc.org/LA6668-3')
concept = node.data
coding = concept.get_coding()[0]
assert isinstance(coding, Coding)
assert coding.get_id() == 'http://loinc.org/LA6668-3'
assert coding.get_code() == 'LA6668-3'
assert coding.get_system() == 'http://loinc.org/'
assert coding.get_display() == 'Pathogenic'
def test_add_concept_by_display():
node=ConceptUsingNode()
node.add_value('Pathogenic')
concept = node.data
coding = concept.get_coding()[0]
assert isinstance(coding, Coding)
assert coding.get_id() == 'http://loinc.org/LA6668-3'
assert coding.get_code() == 'LA6668-3'
assert coding.get_system() == 'http://loinc.org/'
assert coding.get_display() == 'Pathogenic'
def test_add_concept_not_found():
node=ConceptUsingNode()
textval = 'Unknown Text'
node.add_value(textval)
concept = node.data
caught = False
try:
coding = concept.get_coding()[0]
except:
caught = True
assert caught
assert concept.get_text() == textval
def test_add_contrib():
ondate = 'DATESTRING'
role = 'ROLESTRING'
source = {}
sourcetxt = '''
{
"submitted_by": {
"@type": [ "user", "item" ],
"@id": "/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/",
"title": "Amanda Thomas",
"first_name": "Amanda",
"last_name": "Thomas",
"lab": "/labs/curator/",
"uuid": "1db40a7e-e6dc-46dd-9e17-44efbf53d508",
"email": "[email protected]"
}
}
'''
source=json.loads(sourcetxt)
ents = EntityMap(source)
target = MockNode()
add_contribution( source['submitted_by'], target, ondate, ents, role)
contribution = target.contribution
assert isinstance(contribution, Contribution)
agent = contribution.get_agent()
assert agent.get_name() == 'Amanda Thomas'
assert agent.get_id() == IRI_BASE + '/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/'
assert contribution.get_onDate() == ondate
print contribution.get_role()
assert contribution.get_role().get_text() == role
def test_add_contrib_IRI():
tlist = []
ondate = 'DATESTRING'
role = 'ROLESTRING'
source = {}
sourcetxt = '''
{
"previous_user":{
"@id":"/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/",
"@type": ["user"],
"title": "Jed Clampett"
},
"submitted_by": "/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/"
}
'''
source=json.loads(sourcetxt)
ents = EntityMap(source)
subby=source['submitted_by']
target = MockNode()
add_contribution( subby, target, ondate, ents, role)
contribution = target.contribution
agent = contribution.get_agent()
assert agent.get_id() == IRI_BASE + '/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/'
assert agent.get_name() == 'Jed Clampett'
assert contribution.get_onDate() == ondate
assert contribution.get_role().get_text() == role
def test_add_contrib_IRI_only():
tlist = []
ondate = 'DATESTRING'
role = 'ROLESTRING'
source = {}
sourcetxt = '''
{
"submitted_by": "/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/"
}
'''
source=json.loads(sourcetxt)
ents = EntityMap(source)
subby=source['submitted_by']
target = MockNode()
add_contribution( subby, target, ondate, ents, role)
contribution = target.contribution
agent = contribution.get_agent()
assert agent.get_id() == IRI_BASE + '/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/'
assert DMWG_AGENT_NAME_KEY not in agent.data
assert contribution.get_onDate() == ondate
assert contribution.get_role().get_text() == role
def test_canonical_have_car():
carid='http://reg.genome.network/allele/CA229854'
sourcetxt='''
{
"variant": {
"date_created": "2017-03-22T23:03:46.771883+00:00",
"clinVarRCVs": [],
"hgvsNames": {
"GRCh38": "NC_000012.12:g.102846935G>T",
"others": [
"NG_008690.1:g.75668C>A",
"NM_000277.1:c.929C>A",
"NP_000268.1:p.Ser310Tyr",
"P00439:p.Ser310Tyr"
],
"GRCh37": "NC_000012.11:g.103240713G>T"
},
"last_modified": "2017-03-22T23:03:46.771896+00:00",
"clinvarVariantTitle": "NM_000277.1(PAH):c.929C>A (p.Ser310Tyr)",
"source": "ClinVar",
"clinvarVariantId": "102898",
"carId": "%s",
"variationType": "single nucleotide variant",
"molecularConsequenceList": [
{
"term": "missense variant",
"soId": "SO:0001583",
"hgvsName": "NM_000277.1:c.929C>A"
}
],
"@id": "/variants/4cfa029b-3865-47d3-95eb-39e9dffa647b/",
"variant_identifier": "102898",
"submitted_by": "/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/",
"otherDescription": "",
"@type": [
"variant",
"item"
],
"status": "in progress",
"variation_type": "single nucleotide variant",
"clinVarSCVs": [],
"dbSNPIds": [
"62642913"
],
"schema_version": "3",
"associatedPathogenicities": [],
"molecular_consequence": "missense variant",
"uuid": "4cfa029b-3865-47d3-95eb-39e9dffa647b"
}
}''' % carid
source=json.loads(sourcetxt)
ents = EntityMap(source)
rep = canonicalizeVariant(source['variant'])
canonical_id = rep['@id']
assert canonical_id == carid
def test_canonical_no_car():
carid=''
sourcetxt='''
{
"variant": {
"hgvsNames": {
"GRCh38": "NC_000012.12:g.102846935G>T",
"others": [
"NG_008690.1:g.75668C>A",
"NM_000277.1:c.929C>A",
"NP_000268.1:p.Ser310Tyr",
"P00439:p.Ser310Tyr"
],
"GRCh37": "NC_000012.11:g.103240713G>T"
},
"clinvarVariantTitle": "NM_000277.1(PAH):c.929C>A (p.Ser310Tyr)",
"source": "ClinVar",
"clinvarVariantId": "102898",
"carId": "%s",
"@id": "/variants/4cfa029b-3865-47d3-95eb-39e9dffa647b/",
"variant_identifier": "102898",
"@type": [
"variant",
"item"
]
}
}''' % carid
source=json.loads(sourcetxt)
ents = EntityMap(source)
rep = canonicalizeVariant(source['variant'])
canonical_id = rep['@id']
#This is the id that the Baylor Allele Registry returns for this allele.
assert canonical_id == 'http://reg.genome.network/allele/CA229854'
def test_freq_esp():
sourcetxt=''' {
"population": {
"variant": {"@id": "fakeid", "@type": [ "variant", "item" ], "carId": "", "hgvsNames": { "others": [ "NG_009830.1:g.108338C>T", "NM_000051.3:c.6919C>T", "NP_000042.3:p.Leu2307Phe", "Q13315:p.Leu2307Phe", "LRG_135p1:p.Leu2307Phe", "LRG_135t1:c.6919C>T", "LRG_135:g.108338C>T" ], "GRCh37": "NC_000011.9:g.108196896C>T", "GRCh38": "NC_000011.10:g.108326169C>T" } },
"submitted_by": "/users/123",
"last_modified": "2017-03-22T23:05:18.070862+00:00",
"schema_version": "1",
"populationData": {
"desiredCI": 95,
"esp": {
"_tot": { "ac": { "C": 12974, "T": 24 },
"gc": { "CC": 6475, "TC": 24, "TT": 0 } },
"_extra": {
"avg_sample_read": 106,
"rsid": "rs56009889",
"chrom": "11",
"alt": "T",
"hg19_start": 108196896,
"ref": "C" }
}}}}'''
source =json.loads(sourcetxt)
ents = EntityMap(source)
rep = canonicalizeVariant(source['population']['variant'])
canonical_id = rep['@id']
frequencies = transform_frequency( source['population'], ents )
assert len(frequencies) == 1
freqnode = frequencies[0]
#Add getters instead?
assert isinstance(freqnode, AlleleFrequency)
assert freqnode.get_ascertainment().get_coding()[0].get_display() == DMWG_ESP
fpop = freqnode.get_population()
assert isinstance(fpop, CodeableConcept)
codings = fpop.get_coding()
assert len(codings) == 1
popcode = codings[0]
assert isinstance(popcode, Coding)
assert popcode.get_id() == 'http://clinicalgenome.org/datamodel/population-type/combined'
assert freqnode.get_allele().get_id() == canonical_id
assert freqnode.get_alleleCount() == 24
assert freqnode.get_alleleNumber() == 24 + 12974
assert abs(freqnode.get_alleleFrequency() - 24./(24+12974)) < 0.0001
assert freqnode.get_homozygousAlleleIndividualCount() == 0
assert freqnode.get_heterozygousAlleleIndividualCount() == 24
def test_freq_esp_empty():
sourcetxt=''' {
"population": {
"variant": {"@id": "fakeid", "@type": [ "item", "variant" ], "carId": "", "hgvsNames": { "others": [ "NG_009830.1:g.108338C>T", "NM_000051.3:c.6919C>T", "NP_000042.3:p.Leu2307Phe", "Q13315:p.Leu2307Phe", "LRG_135p1:p.Leu2307Phe", "LRG_135t1:c.6919C>T", "LRG_135:g.108338C>T" ], "GRCh37": "NC_000011.9:g.108196896C>T", "GRCh38": "NC_000011.10:g.108326169C>T" }},
"schema_version": "1",
"submitted_by": "/users/123",
"last_modified": "2017-03-22T23:05:18.070862+00:00",
"populationData": {
"desiredCI": 95,
"esp": {
"_tot": { "ac": {}, "gc":{} },
"_extra": {}
}}}}'''
source =json.loads(sourcetxt)
ents = EntityMap(source)
rep = canonicalizeVariant(source['population']['variant'])
canonical_id = rep['@id']
freqs = transform_frequency( source['population'], ents )
assert len(freqs) == 1
freq = freqs[0]
assert isinstance(freq, AlleleFrequency)
assert freq.get_allele().get_id() == canonical_id
assert freq.get_alleleCount() == 0
assert freq.get_alleleNumber() == 0
def test_freq_exac():
sourcetxt=''' {
"population": {
"variant": {"@id": "fakeid", "@type": [ "item", "variant" ] , "carId": "", "hgvsNames": { "others": [ "NG_009830.1:g.108338C>T", "NM_000051.3:c.6919C>T", "NP_000042.3:p.Leu2307Phe", "Q13315:p.Leu2307Phe", "LRG_135p1:p.Leu2307Phe", "LRG_135t1:c.6919C>T", "LRG_135:g.108338C>T" ], "GRCh37": "NC_000011.9:g.108196896C>T", "GRCh38": "NC_000011.10:g.108326169C>T" }},
"submitted_by": "/users/123",
"last_modified": "2017-03-22T23:05:18.070862+00:00",
"schema_version": "1",
"populationData": {
"desiredCI": 95,
"exac": {
"amr": {
"an": 11574,
"af": 0.00017280110592707794,
"ac": 2,
"hom": 0
},
"eas": {
"an": 8642,
"af": 0,
"ac": 0,
"hom": 0
},
"afr": {
"an": 10404,
"af": 0.00009611687812379854,
"ac": 1,
"hom": 0
},
"_tot": {
"an": 121374,
"af": 0.0011040255738461284,
"ac": 134,
"hom": 1
},
"_extra": {
"pos": 108196896,
"alt": "T",
"ref": "C",
"chrom": "11"
}
}}}}'''
source =json.loads(sourcetxt)
ents = EntityMap(source)
rep = canonicalizeVariant(source['population']['variant'])
canonical_id = rep['@id']
freqs = transform_frequency( source['population'], ents )
assert len(freqs) == 4
prefix = 'http://broadinstitute.org/populations/%s'
chex = { prefix % 'amr': (11574, 0.000172, 2, 0),\
prefix % 'eas': (8642, 0., 0, 0), \
prefix % 'afr': (10404, 0.000096, 1, 0), \
'http://clinicalgenome.org/datamodel/population-type/combined': (121374, 0.001104, 134, 1) }
for freq in freqs:
assert isinstance(freq, AlleleFrequency)
assert freq.get_ascertainment().get_coding()[0].get_id() == 'http://clinicalgenome.org/datamodel/ascertainment-type/ExAC'
values = chex[freq.get_population().get_coding()[0].get_id()]
assert freq.get_allele().get_id() == canonical_id
assert freq.get_alleleCount() == values[2]
assert freq.get_alleleNumber() == values[0]
assert abs(freq.get_alleleFrequency()- values[1]) < 0.0001
assert freq.get_homozygousAlleleIndividualCount() == values[3]
def test_thousandGenomes():
src='''
{
"population": {
"variant": {"@id": "fakeid", "@type": [ "item", "variant" ] , "carId": "", "hgvsNames": { "GRCh37": "NC_000012.11:g.103310879G>C", "GRCh38": "NC_000012.12:g.102917101G>C" }},
"schema_version": "1",
"submitted_by": "/users/123",
"last_modified": "2017-03-22T23:05:18.070862+00:00",
"populationData": {
"desiredCI": 95,
"tGenomes": {
"amr": { "af": { "G": 1 }, "gc": { "G|G": 347 }, "gf": { "G|G": 1 }, "ac": { "G": 694 } },
"eas": { "af": { "G": 1 }, "gc": { "G|G": 504 }, "gf": { "G|G": 1 }, "ac": { "G": 1008 } },
"_extra": { "var_class": "SNP", "name": "rs1801145", "alt": "C", "ref": "G" },
"afr": { "af": { "G": 1 }, "gc": { "G|G": 661 }, "gf": { "G|G": 1 }, "ac": { "G": 1322 } },
"espaa": { "af": { "G": 1 }, "gc": {}, "gf": {}, "ac": { "G": 4406 } },
"eur": { "af": { "G": 0.999005964214712, "C": 0.00099403578528827 }, "gc": { "G|G": 502, "C|G": 1 }, "gf": { "G|G": 0.998011928429423, "C|G": 0.00198807157057654 }, "ac": { "G": 1005, "C": 1 } },
"espea": { "af": { "G": 0.999302, "C": 0.000697674 }, "gc": {}, "gf": {}, "ac": { "G": 8594, "C": 6 } },
"_tot": { "af": { "G": 0.999800319488818, "C": 0.000199680511182109 }, "gc": { "G|G": 2503, "C|G": 1 }, "gf": { "G|G": 0.999600638977636, "C|G": 0.000399361022364217 }, "ac": { "G": 5007, "C": 1 } },
"sas": { "af": { "G": 1 }, "gc": { "G|G": 489 }, "gf": { "G|G": 1 }, "ac": { "G": 978 } }
}
}
} }'''
source = json.loads(src)
ents = EntityMap(source)
rep= canonicalizeVariant(source['population']['variant'])
canonical_id = rep['@id']
freqs = transform_frequency( source['population'], ents)
assert len(freqs) == 8
p1 = 'http://www.internationalgenome.org/category/population/%s'
p2 = 'http://evs.gs.washington.edu/EVS/%s'
comb = 'http://clinicalgenome.org/datamodel/population-type/combined'
DMWG_1000_GENOMES = 'http://clinicalgenome.org/datamodel/ascertainment-type/1KG'
DMWG_1000_GENOMES_ESP = 'http://clinicalgenome.org/datamodel/ascertainment-type/1KG_ESP'
ex = { p1 % 'amr': (DMWG_1000_GENOMES,694, 0., 0, 0),\
p1 % 'eas': (DMWG_1000_GENOMES,1008, 0., 0, 0), \
p1 % 'afr': (DMWG_1000_GENOMES,1322, 0., 0, 0), \
p2 % 'AA': (DMWG_1000_GENOMES_ESP,4406, 0., 0, 0), \
p1 % 'eur': (DMWG_1000_GENOMES,1006, 0.000994, 1, 0), \
p2 % 'EA': (DMWG_1000_GENOMES_ESP,8600, 0.000697, 6, 0), \
comb: (DMWG_1000_GENOMES,5008, 0.0001996, 1, 0),
p1 % 'sas': (DMWG_1000_GENOMES,978, 0., 0, 0) }
for freq in freqs:
assert freq.get_allele().get_id() == canonical_id
values = ex[freq.get_population().get_coding()[0].get_id()]
assert freq.get_ascertainment().get_coding()[0].get_id() == values[0]
assert freq.get_alleleNumber() == values[1]
assert abs(freq.get_alleleFrequency()- values[2]) < 0.0001
assert freq.get_alleleCount() == values[3]
assert freq.get_homozygousAlleleIndividualCount() == values[4]
def test_conservation():
sourcetext='''
{
"variant": {
"hgvsNames": { "GRCh38": "NC_000012.12:g.102846935G>T" },
"@id": "/variants/4cfa029b-3865-47d3-95eb-39e9dffa647b/",
"@type": [ "variant", "item" ],
"carId":""
},
"computational": {
"@id": "/computational/d9d3e60d-50b1-424b-8bcc-c892bba0da22/",
"@type": ["item", "data"],
"last_modified": "2017-03-22T23:08:28.110287+00:00",
"variant": "/variants/4cfa029b-3865-47d3-95eb-39e9dffa647b/",
"computationalData": {
"conservation": {
"phylop20way": "0.948",
"phylop7way": "9.598",
"phastconsp20way": "0.953",
"siphy": "19.1358",
"gerp": "5.38",
"phastconsp7way": "1"
}
},
"submitted_by": {
"first_name": "Amanda",
"last_name": "Thomas",
"title": "Amanda Thomas",
"@id": "/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/",
"@type": ["user", "item"]
}
}}'''
source = json.loads(sourcetext)
ents = EntityMap(source)
print source['variant'], type(source['variant'])
rep = canonicalizeVariant(source['variant'])
canonical_id = rep['@id']
comps = transform_computational( source['computational'], ents)
assert len(comps) == 6
chex={"phylop20way": '0.948', \
"phylop7way": '9.598', \
"phastconsp20way": '0.953', \
"siphy": '19.1358', \
"gerp": '5.38', \
"phastconsp7way": '1' }
for comp in comps:
assert comp.get_allele().get_id() == canonical_id
score = chex[ comp.get_algorithm() ]
assert comp.get_score()== score