def test_transform_variant(self):
variant = GeneVariant(expr='NC_000001.10:g.11856378G>A')
assert variant.transform_variant(
GeneVariant.TRANSFORM_CHR_POS_REF_ALT) == [
'1', '11856378', 'G', 'A'
]
assert variant.transform_variant(
GeneVariant.TRANSFORM_CHR_POS) == ['1', '11856378']
def test_get_variant_url(self):
variant = GeneVariant('chr1:g.11856378G>A')
assert GnomAD.get_variant_url(
variant) == GnomAD.VARIANT_ROUTE + '1-11856378-G-A'
variant = GeneVariant('NM_001098210.1:c.241+6_241+7del')
assert GnomAD.get_variant_url(
variant) == GnomAD.VARIANT_ROUTE + '3-41266247-AAG-A'
variant = GeneVariant('NC_000003.11:g.41266248_41266249delAG')
assert GnomAD.get_variant_url(
variant) == GnomAD.VARIANT_ROUTE + '3-41266247-AAG-A'
def test_type(self):
variant = GeneVariant(expr='NM_005957.4:c.665C>T')
assert variant.ref_type == GeneVariant.REF_TYPE_NM
variant = GeneVariant(expr='ENST_005957.4:c.665C>T')
assert variant.ref_type == GeneVariant.REF_TYPE_ENST
variant = GeneVariant(expr='NC_005957.4:c.665C>T')
assert variant.ref_type == GeneVariant.REF_TYPE_NC
variant = GeneVariant(expr='NP_005957.4:c.665C>T')
assert variant.ref_type == GeneVariant.REF_TYPE_NP
variant = GeneVariant(expr='chr1:g.11856378G>A')
assert variant.ref_type == GeneVariant.REF_TYPE_CHR
def test_search_variants(self):
variant = GeneVariant("chr1:g.114716127G>A")
assert COSMIC.search_variant_db(variant=variant, only_count=True) > 0
# cDNA
variant = GeneVariant("ENST00000376236:c.1089C>T")
assert COSMIC.search_variant_db(variant=variant, only_count=True) > 0
variant = GeneVariant("ENST00000376236:p.N363N")
assert COSMIC.search_variant_db(variant=variant, only_count=True) > 0
variant = GeneVariant("ENST00000376236:p.Asn363Asn")
assert COSMIC.search_variant_db(variant=variant, only_count=True) > 0
def test_init(self):
with pytest.raises(ValueError) as excinfo:
GeneVariant()
with pytest.raises(ValueError) as excinfo:
GeneVariant(ref_seq='NM_005957.4')
with pytest.raises(ValueError) as excinfo:
GeneVariant(var_info='c.665C>T')
with pytest.raises(ValueError) as excinfo:
GeneVariant(expr='ABC_1234')
with pytest.raises(ValueError) as excinfo:
GeneVariant(ref_seq='ABC_1234', var_info='c.665C>T')
GeneVariant(ref_seq='NM_005957.4', var_info='c.665C>T')
GeneVariant(expr='NM_005957.4:c.665C>T')
def test_transform_ref_seq_else(self):
variant = GeneVariant(expr='chr1:g.11856378G>A')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_NM)
variant = GeneVariant(expr='chr1:g.11856378G>A')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_NP)
variant = GeneVariant(expr='chr1:g.11856378G>A')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_NC)
variant = GeneVariant(expr='NM_005957.4:c.665C>T')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_CHR)
variant = GeneVariant(expr='NP_005948.3:p.Ala222Val')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_CHR)
variant = GeneVariant(expr='NC_000001.10:g.11856378G>A')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_CHR)
def test_transform_ref_seq_ENST(self):
variant = GeneVariant(expr='NM_005957.4:c.665C>T')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_ENST)
variant = GeneVariant(expr='ENST00000376590:c.665C>T')
assert variant.transform_ref_seq(GeneVariant.REF_TYPE_NM)
def test_search_variant_local(self):
variant = GeneVariant('PTEN:c.697C>T')
res = MyCancerGenome.search_variant_local(variant)
assert res and res['variant_match'] == True and res[
'url'] == 'https://www.mycancergenome.org/content/gene/PTEN'
def test_search_variant(self):
variant = GeneVariant('chr1:g.11856378G>A')
assert DECIPHER.get_variant_url(
variant
) == 'https://decipher.sanger.ac.uk/search?q=1%3A11856378#consented-patients/results'
def test_search_variant(self):
variant = GeneVariant('chr1:g.11856378G>A')
assert GTEx.get_variant_url(
variant) == GTEx.VARIANT_ROUTE + 'rs1801133'
def test_search_variant(self):
variant = GeneVariant('chr1:g.11856378G>A')
assert CIViC.search_variant(variant)
def test_search_variant(self):
variant = GeneVariant('chr7:g.140453134T>C')
res = GDC.search_variant(variant)
assert res and res[
'url'] == 'https://portal.gdc.cancer.gov/ssms/3d2daeb9-3ede-594a-8a84-c84e7fd453df'
def search_sources(target_str, search_type):
redis_key = None
if search_type == TYPE_GENE or search_type == TYPE_TRANSCRIPT:
target = GeneReference(target_str)
redis_gene_name = target.transform_ref_seq(GeneReference.REF_TYPE_GENE)
if redis_gene_name:
redis_key = redis_gene_name
elif search_type == TYPE_VARIANT:
target = GeneVariant(target_str)
redis_gene_name = target.transform_ref_seq(GeneReference.REF_TYPE_GENE)
c_info = target.transform_variant(target.ref_type,
GeneVariant.INFO_TYPE_C)[1]
if redis_gene_name and c_info:
redis_key = redis_gene_name + ':' + c_info
else:
raise ValueError("Invalid search type")
if redis_key:
search_result = REDIS_SEARCH.get(redis_key)
if search_result:
print 'READ FROM REDIS CACHE'
return json.loads(search_result)
mv_res = target.get_myvariant_res()
res = {MY_VARIANT: mv_res, SOURCE_NAMES_KEY: {}}
for source in GENE_SOURCES:
time_start = time.clock()
if search_type == TYPE_GENE:
source_res = source.search_gene(target)
elif search_type == TYPE_VARIANT:
source_res = source.search_variant(target)
elif search_type == TYPE_TRANSCRIPT:
source_res = source.search_transcript(target)
if search_type == TYPE_VARIANT and not source_res:
source_res = source.search_transcript(target)
if source_res:
source_res['downgrade'] = 'Transcript'
if search_type != TYPE_GENE and not source_res:
source_res = source.search_gene(target)
if source_res:
source_res['downgrade'] = 'Gene'
res[source.__name__.lower()] = source_res
res[SOURCE_NAMES_KEY][source.__name__.lower()] = source.__name__
time_elapsed = (time.clock() - time_start)
print source.__name__ + ' takes time ' + str(time_elapsed)
prepare_source_report(res, search_type)
report = res[REPORT_KEY]
time_start = time.clock()
all_ids = target.get_all_ids()
time_elapsed = (time.clock() - time_start)
print 'All ids takes time ' + str(time_elapsed)
report[IDS_KEY] = all_ids
if search_type == TYPE_VARIANT:
aa = target.get_aa()
print aa
if aa[0] and aa[1]:
# calculate grantham score
def translate_grantham_score(score):
if score > 150:
return unicode(_("Radical Substitution"))
elif score <= 150 and score > 100:
return unicode(_("Moderately Radical Substitution"))
elif score <= 100 and score > 50:
return unicode(_("Moderately Conservative Substitution"))
elif score <= 50 and score >= 0:
return unicode(_("Conservative Substitution"))
return 'N/A'
grantham_score = GeneVariant.calculate_grantham_score(ref_aa=aa[0],
alt_aa=aa[1])
report[GRANTHAM_SCORE_KEY] = grantham_score
report[GRANTHAM_INFO_KEY] = translate_grantham_score(
grantham_score)
# add in aa info
report[REF_AA_KEY] = aa[0]
report[ALT_AA_KEY] = aa[1]
# save to redis
if redis_key:
REDIS_SEARCH.set(redis_key, json.dumps(res),
ex=2073600) # TODO: Current: 1day
return res