def test_convert_bidirectionally_hgvs_c_variation_id(self):
variation_id = 47706
hgvs_text = 'NM_133378.4:c.98772T>C'
assert_that(variation_id in ClinvarVariationID(hgvs_text))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_text))
assert_that(hgvs_text in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405_find_hgvs_for_previously_entered_LRG_slang_sloppy_variant_name(self):
hgvs_c = 'NM_004006.2:c.5586+18A>G'
variation_id = 94672
allele_id = 100572
accession = 'RCV000080662'
assert_that(accession in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_413_accession_and_variation_id_for_hgvs_c(self):
hgvs_c = 'NM_001232.3:c.919G>C'
allele_id = 32649
variation_id = 17610
accession = 'RCV000019176'
assert_that(accession in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405_hgvs_c_was_null_slang_used_in_variant_name(self):
hgvs_c = 'NM_002485.4:c.1222A>G'
variation_id = 127856
allele_id = 133313
accession1 = 'RCV000115778'
accession2 = 'RCV000119194'
assert_that(accession1 in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(accession2 in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def main():
global UNUSABLE
global GOOD
db = ClinVarDB()
# hello, are you there MySQL? It's me, python.
db.ping()
print('(Re)creating clinvar component table', TARGET_TABLENAME)
db.drop_table(TARGET_TABLENAME)
db.execute("call log('components', 'creating " + TARGET_TABLENAME +
" table')")
db.execute('''create table ''' + TARGET_TABLENAME + ''' (
id int(11) primary key auto_increment,
VariationID int(11),
hgvs_text varchar(255),
PMID int(11) default null,
GeneID int(11) default null,
Symbol varchar(20) default null,
Ref varchar(10) default null,
Pos int(11) default null,
Alt varchar(10) default null,
EditType varchar(25) default null,
SeqType varchar(10) default null)''')
log.info('Rebuilding %s', TARGET_TABLENAME)
log.info('Creating unique index on PMID-hgvs_text')
db.execute('ALTER TABLE ' + TARGET_TABLENAME +
' ADD UNIQUE INDEX pmid_hgvs (PMID, hgvs_text)')
try:
res = db.fetchrow('select count(*) as cnt from %s' % SOURCE_TABLENAME)
except Exception as error:
print(error)
log.debug('%r' % error)
sys.exit()
log.info('Rows in %s: %i' % (SOURCE_TABLENAME, res['cnt']))
rows = db.fetchall('select * from ' + SOURCE_TABLENAME +
' order by rand()')
count = 0
total_added = 0
for row in rows:
count += 1
print(count, '/', res['cnt'], ':', row['variant_name'])
results = process_row(db, row)
if len(results) == 0:
UNUSABLE += 1
else:
GOOD += 1
total_added += len(results)
return len(rows), total_added
def setUp(self):
self.db = ClinVarDB()
class TestClinVarDB(TestCase):
def setUp(self):
self.db = ClinVarDB()
def test_get_random_example_hgvs(self):
examples = self.db.random_example_hgvs()
assert_that(len(examples), equal_to(1))
examples = self.db.random_example_hgvs(10)
assert_that(len(examples), equal_to(10))
assert_that(examples[0], starts_with('NM_'))
print examples
def test_BIOMED_310_citations_specific_to_clinvar(self):
pubmeds = ClinvarPubmeds('NM_000410.3:c.845G>A')
assert_that(len(pubmeds) > 35)
assert_that(10673304, is_in(pubmeds))
assert_that(9439654, is_in(pubmeds))
def test_convert_bidirectionally_hgvs_c_variation_id(self):
variation_id = 47706
hgvs_text = 'NM_133378.4:c.98772T>C'
assert_that(variation_id in ClinvarVariationID(hgvs_text))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_text))
assert_that(hgvs_text in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_convert_pubmed_central_PMCID_to_pubmed_PMID(self):
pmcid = int(3110945)
pmid = int(15371902)
assert_that(int(PMCID2Article(pmcid).pmid), equal_to(pmid))
hgvs_text = 'NM_000492.3:c.1519_1521delATC'
assert_that(pmid in ClinvarPubmeds(hgvs_text))
assert_that(pmcid not in ClinvarPubmeds(hgvs_text))
# NKF - 8/11/15 - commented out test due to NCBI Variant Reporter being down
def _test_well_cited_variant_has_some_different_clinvar_dbsnp_entries(self):
hgvs_text = 'NM_000492.3:c.1521_1523delCTT'
ncbi_pmids = NCBIVariantPubmeds(hgvs_text)
ncbi_pmids = set([int(entry) for entry in ncbi_pmids])
clinvar_pmids = ClinvarPubmeds(hgvs_text)
# This paper is cited by dbSNP but not ClinVar
#
# Proof:
# http://www.ncbi.nlm.nih.gov/snp?LinkName=pubmed_snp_cited&from_uid=15948195
#
assert_that(15948195 in ncbi_pmids)
assert_that(15948195 not in clinvar_pmids)
# ClinVar knows about this PMID but Variation Reporter does not.
# Probably because it is cited by PubMedCentral and not Pubmed.
#
assert_that(15371902 in clinvar_pmids)
assert_that(15371902 not in ncbi_pmids)
assert_that(15371902, equal_to(int(PMCID2Article(3110945).pmid)))
def test_BIOMED_413_accession_and_variation_id_for_hgvs_c(self):
hgvs_c = 'NM_001232.3:c.919G>C'
allele_id = 32649
variation_id = 17610
accession = 'RCV000019176'
assert_that(accession in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405_hgvs_c_was_null_slang_used_in_variant_name(self):
hgvs_c = 'NM_002485.4:c.1222A>G'
variation_id = 127856
allele_id = 133313
accession1 = 'RCV000115778'
accession2 = 'RCV000119194'
assert_that(accession1 in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(accession2 in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405_find_hgvs_for_previously_entered_LRG_slang_sloppy_variant_name(self):
hgvs_c = 'NM_004006.2:c.5586+18A>G'
variation_id = 94672
allele_id = 100572
accession = 'RCV000080662'
assert_that(accession in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405__has_accession_for_previously_null_hgvs_c(self):
hgvs_text = 'NM_000016.4:c.1091T>C'
accession = 'RCV000077876'
variation_id = 92253
pmid = 23757202
assert_that(accession in ClinvarAccession(hgvs_text))
assert_that(variation_id in ClinvarVariationID(hgvs_text))
assert_that(pmid in ClinvarPubmeds(hgvs_text))
def test_BIOMED_405__new_hgvs_c_entry_for_previously_null_hgvs_c(self):
for hgvs_text in [
# 'NM_138370.1:c.168C>T',
'NM_058216.1:c.706-2A>G'
, 'NM_001099404.1:c.3556G>A'
#, 'NM_001033756.2:c.963-1174C>T'
, 'NM_181798.1:c.785C>A'
, 'NM_000368.3:c.1579C>T'
#, 'NM_001164883.1:c.2298+14940A>G'
#, 'NM_152404.3:c.577G>A'
, 'NM_000314.4:c.170T>G'
, 'NM_198056.2:c.3907C>A'
, 'NM_023035.2:c.4375G>T'
, 'NM_000257.2:c.2683C>G'
, 'NM_000060.2:c.1227_1241delins11'
#, 'NM_001130455.1:c.564G>A'
#, 'NM_003815.4:c.840C>T'
, 'NM_001267550.1:c.67571G>A'
, 'NM_000057.2:c.1544dupA'
, 'NM_007294.3:c.2679_2682del'
#, 'NM_020142.3:c.-264-u3504C>T'
]:
print hgvs_text
assert_that(len(ClinvarVariationID(hgvs_text)) >= 1)
assert_that(len(ClinvarAccession(hgvs_text)) >= 1)
# NKF - 8/11/15 - commented out test due to NCBI Variant Reporter being down
def _test_BIOMED_405__haplotype_has_multiple_variation_id_for_single_hgvs(self):
hgvs_text = 'NM_000060.2:c.133G>A'
pmid_expected = NCBIVariantPubmeds(hgvs_text)
pmid_expected = set([int(id) for id in pmid_expected])
assert_that(3 == len(ClinvarVariationID(hgvs_text)))
assert_that(1 == len(ClinvarAlleleID(hgvs_text)))
assert_that(3 == len(ClinvarPubmeds(hgvs_text)))
assert_that(set(ClinvarPubmeds(hgvs_text)) == pmid_expected)
def test_get_version(self):
version_str = self.db.get_version()
assert_that(len(version_str), greater_than(0))
class TestClinVarDB(TestCase):
def setUp(self):
self.db = ClinVarDB()
def test_get_random_example_hgvs(self):
examples = self.db.random_example_hgvs()
assert_that(len(examples), equal_to(1))
examples = self.db.random_example_hgvs(10)
assert_that(len(examples), equal_to(10))
assert_that(examples[0], starts_with('NM_'))
#print examples
def test_bookID_citations_specific_to_clinvar(self):
pubmeds = ClinvarPubmeds('NM_000410.3:c.845G>A')
assert_that(len(pubmeds) > 35)
assert_that('NBK1440', is_in(pubmeds))
def test_convert_bidirectionally_hgvs_c_variation_id(self):
variation_id = 47706
hgvs_text = 'NM_133378.4:c.98772T>C'
assert_that(variation_id in ClinvarVariationID(hgvs_text))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_text))
assert_that(hgvs_text in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_convert_pubmed_central_PMCID_to_pubmed_PMID(self):
pmcid = int(3110945)
pmid = int(15371902)
assert_that(int(PMCID2Article(pmcid).pmid), equal_to(pmid))
def test_BIOMED_413_accession_and_variation_id_for_hgvs_c(self):
hgvs_c = 'NM_001232.3:c.919G>C'
allele_id = 32649
variation_id = 17610
accession = 'RCV000019176'
assert_that(accession in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405_hgvs_c_was_null_slang_used_in_variant_name(self):
hgvs_c = 'NM_002485.4:c.1222A>G'
variation_id = 127856
allele_id = 133313
accession1 = 'RCV000115778'
accession2 = 'RCV000119194'
assert_that(accession1 in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(accession2 in ClinVarDB().accession_for_hgvs_text(hgvs_c))
assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
#def test_BIOMED_405_find_hgvs_for_previously_entered_LRG_slang_sloppy_variant_name(self):
# hgvs_c = 'NM_004006.2:c.5586+18A>G'
# variation_id = 94672
# allele_id = 100572
# accession = 'RCV000080662'
# assert_that(accession in ClinVarDB().accession_for_hgvs_text(hgvs_c))
# assert_that(variation_id in ClinVarDB().variation_id_for_hgvs_text(hgvs_c))
# assert_that(allele_id in ClinVarDB().allele_id_for_hgvs_text(hgvs_c))
# assert_that(hgvs_c in ClinVarDB().hgvs_text_for_variation_id(variation_id))
def test_BIOMED_405__has_accession_for_previously_null_hgvs_c(self):
hgvs_text = 'NM_000016.4:c.1091T>C'
accession = 'RCV000077876'
variation_id = 92253
#TODO: replace this PMID (no longer valid)
#pmid = 23757202
#assert_that(pmid in ClinvarPubmeds(hgvs_text))
assert_that(accession in ClinvarAccession(hgvs_text))
assert_that(variation_id in ClinvarVariationID(hgvs_text))
def test_get_version(self):
version_str = self.db.get_version()
assert_that(len(version_str), greater_than(0))