def test_mafip(mafip, hgnc):
"""Test that mafip normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:31102')
check_resp_single_record(resp, mafip, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('MAFIP')
check_resp_single_record(resp, mafip, MatchType.SYMBOL)
def test_gage4(gage4, hgnc):
"""Test that gage4 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:4101')
check_resp_single_record(resp, gage4, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('GAGE4')
check_resp_single_record(resp, gage4, MatchType.SYMBOL)
def test_hdpa(ncbi, hdpa):
"""Test that HDPA normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:50829')
check_resp_single_record(resp, hdpa, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('HDPA')
check_resp_single_record(resp, hdpa, MatchType.SYMBOL)
def test_trl_cag2_1(trl_cag2_1, hgnc):
"""Test that trl_cag2_1 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:34692')
check_resp_single_record(resp, trl_cag2_1, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('TRL-CAG2-1')
check_resp_single_record(resp, trl_cag2_1, MatchType.SYMBOL)
def test_loc106783576(ncbi, loc106783576):
"""Test that LOC106783576 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:106783576')
check_resp_single_record(resp, loc106783576, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('LOC106783576')
check_resp_single_record(resp, loc106783576, MatchType.SYMBOL)
def test_cecr(cecr, hgnc):
"""Test that cecr normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:1838')
check_resp_single_record(resp, cecr, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('CECR')
check_resp_single_record(resp, cecr, MatchType.SYMBOL)
def test_slc25a6(ncbi, slc25a6):
"""Test that SLC25A6 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:293')
check_resp_single_record(resp, slc25a6, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('SLC25A6')
check_resp_single_record(resp, slc25a6, MatchType.SYMBOL)
def test_znf84(ncbi, znf84):
"""Test that ZNF84 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:7637')
check_resp_single_record(resp, znf84, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('ZNF84')
check_resp_single_record(resp, znf84, MatchType.SYMBOL)
def test_afa(ncbi, afa):
"""Test that AFA normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:170')
check_resp_single_record(resp, afa, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('AFA')
check_resp_single_record(resp, afa, MatchType.SYMBOL)
def test_pirc24(pirc24, hgnc):
"""Test that pirc24 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:37528')
check_resp_single_record(resp, pirc24, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('PIRC24')
check_resp_single_record(resp, pirc24, MatchType.SYMBOL)
def test_mt_7sdna(mt_7sdna, hgnc):
"""Test that mt_7sdna normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:7409')
check_resp_single_record(resp, mt_7sdna, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('MT-7SDNA')
check_resp_single_record(resp, mt_7sdna, MatchType.SYMBOL)
def test_wdhd1(wdhd1, hgnc):
"""Test that a1bg_as1 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:23170')
check_resp_single_record(resp, wdhd1, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('WDHD1')
check_resp_single_record(resp, wdhd1, MatchType.SYMBOL)
def test_csf2ra(csf2ra, hgnc):
"""Test that csf2ra normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:2435')
check_resp_single_record(resp, csf2ra, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('CSF2RA')
check_resp_single_record(resp, csf2ra, MatchType.SYMBOL)
def test_adcp1(ncbi, adcp1):
"""Test that ADCP1 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:106')
check_resp_single_record(resp, adcp1, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('ADCP1')
check_resp_single_record(resp, adcp1, MatchType.SYMBOL)
def test_rps24p5(rps24p5, hgnc):
"""Test that rps24p5 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:36026')
check_resp_single_record(resp, rps24p5, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('rpS24P5')
check_resp_single_record(resp, rps24p5, MatchType.SYMBOL)
def test_g6pr(g6pr, hgnc):
"""Test that g6pr normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:4059')
check_resp_single_record(resp, g6pr, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('G6PR')
check_resp_single_record(resp, g6pr, MatchType.SYMBOL)
def test_ddx11l1(ensembl, ddx11l1):
"""Test that DDX11L1 normalizes to correct gene concept."""
# Concept ID
resp = ensembl.search("ensembl:ENSG00000223972")
check_resp_single_record(resp, ddx11l1, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSEMBL:ENSG00000223972")
check_resp_single_record(resp, ddx11l1, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSG00000223972")
check_resp_single_record(resp, ddx11l1, MatchType.CONCEPT_ID)
# Symbol
resp = ensembl.search("ddx11l1")
check_resp_single_record(resp, ddx11l1, MatchType.SYMBOL)
resp = ensembl.search("DDX11L1")
check_resp_single_record(resp, ddx11l1, MatchType.SYMBOL)
def test_tp53(ensembl, tp53):
"""Test that tp53 normalizes to correct gene concept."""
# Concept ID
resp = ensembl.search("ensembl:ENSG00000141510")
check_resp_single_record(resp, tp53, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSEMBL:ENSG00000141510")
check_resp_single_record(resp, tp53, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSG00000141510")
check_resp_single_record(resp, tp53, MatchType.CONCEPT_ID)
# Symbol
resp = ensembl.search("tp53")
check_resp_single_record(resp, tp53, MatchType.SYMBOL)
resp = ensembl.search("TP53")
check_resp_single_record(resp, tp53, MatchType.SYMBOL)
def test_hsa_mir_1253(ensembl, hsa_mir_1253):
"""Test that hsa-mir-1253 normalizes to correct gene concept."""
# Concept ID
resp = ensembl.search("ensembl:ENSG00000272920")
check_resp_single_record(resp, hsa_mir_1253, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSEMBL:ENSG00000272920")
check_resp_single_record(resp, hsa_mir_1253, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSG00000272920")
check_resp_single_record(resp, hsa_mir_1253, MatchType.CONCEPT_ID)
# Symbol
resp = ensembl.search("hsa-mir-1253")
check_resp_single_record(resp, hsa_mir_1253, MatchType.SYMBOL)
# associated_with
resp = ensembl.search("mirbase:MI0006387")
check_resp_single_record(resp, hsa_mir_1253, MatchType.ASSOCIATED_WITH)
def test_CH17_340M24_3(ensembl, CH17_340M24_3):
"""Test that CH17-340M24.3 normalizes to correct gene concept."""
# Concept ID
resp = ensembl.search('ensembl:ENSG00000197180')
check_resp_single_record(resp, CH17_340M24_3, MatchType.CONCEPT_ID)
resp = ensembl.search('ENSEMBL:ENSG00000197180')
check_resp_single_record(resp, CH17_340M24_3, MatchType.CONCEPT_ID)
resp = ensembl.search('ENSG00000197180')
check_resp_single_record(resp, CH17_340M24_3, MatchType.CONCEPT_ID)
# Symbol
resp = ensembl.search('CH17-340M24.3')
check_resp_single_record(resp, CH17_340M24_3, MatchType.SYMBOL)
def test_ATP6AP1_DT(ensembl, ATP6AP1_DT):
"""Test that ATP6AP1-DT normalizes to correct gene concept."""
# Concept ID
resp = ensembl.search("ensembl:ENSG00000197180")
check_resp_single_record(resp, ATP6AP1_DT, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSEMBL:ENSG00000197180")
check_resp_single_record(resp, ATP6AP1_DT, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSG00000197180")
check_resp_single_record(resp, ATP6AP1_DT, MatchType.CONCEPT_ID)
# Symbol
resp = ensembl.search("ATP6AP1-DT")
check_resp_single_record(resp, ATP6AP1_DT, MatchType.SYMBOL)
def test_spry3(ensembl, spry3):
"""Test that spry3 normalizes to correct gene concept."""
# Concept ID
resp = ensembl.search("ensembl:EnSG00000168939")
check_resp_single_record(resp, spry3, MatchType.CONCEPT_ID)
resp = ensembl.search("ENSEMBL:EnSG00000168939")
check_resp_single_record(resp, spry3, MatchType.CONCEPT_ID)
resp = ensembl.search("EnSG00000168939")
check_resp_single_record(resp, spry3, MatchType.CONCEPT_ID)
# Symbol
resp = ensembl.search("spry3")
check_resp_single_record(resp, spry3, MatchType.SYMBOL)
def test_glc1b(ncbi, glc1b):
"""Test that GLC1B normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:2722')
check_resp_single_record(resp, glc1b, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('GLC1B')
check_resp_single_record(resp, glc1b, MatchType.SYMBOL)
# associated_with
resp = ncbi.search('omim:606689')
check_resp_single_record(resp, glc1b, MatchType.ASSOCIATED_WITH)
def test_prkrap1(ncbi, prkrap1):
"""Test that PRKRAP1 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:731716')
check_resp_single_record(resp, prkrap1, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('PRKRAP1')
check_resp_single_record(resp, prkrap1, MatchType.SYMBOL)
# xref
resp = ncbi.search('hgnc:33447')
check_resp_single_record(resp, prkrap1, MatchType.XREF)
def test_mhb(ncbi, mhb):
"""Test that MHB normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:619511')
check_resp_single_record(resp, mhb, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('MHB')
check_resp_single_record(resp, mhb, MatchType.SYMBOL)
# associated_with
resp = ncbi.search('OMIM:255160')
check_resp_single_record(resp, mhb, MatchType.ASSOCIATED_WITH)
def test_spg37(ncbi, spg37):
"""Test that SPG37 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:100049159')
check_resp_single_record(resp, spg37, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('SPG37')
check_resp_single_record(resp, spg37, MatchType.SYMBOL)
# associated_with
resp = ncbi.search('omim:611945')
check_resp_single_record(resp, spg37, MatchType.ASSOCIATED_WITH)
def test_gstt1(gstt1, hgnc):
"""Test that gstt1 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:4641')
check_resp_single_record(resp, gstt1, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('GSTT1')
check_resp_single_record(resp, gstt1, MatchType.SYMBOL)
# associated_with
resp = hgnc.search('omim:600436')
check_resp_single_record(resp, gstt1, MatchType.ASSOCIATED_WITH)
def test_myo5b(myo5b, hgnc):
"""Test that myo5b normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:7603')
check_resp_single_record(resp, myo5b, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('MYO5B')
check_resp_single_record(resp, myo5b, MatchType.SYMBOL)
# associated_with
resp = hgnc.search('refseq:NM_001080467')
check_resp_single_record(resp, myo5b, MatchType.ASSOCIATED_WITH)
def test_spry3(ncbi, spry3):
"""Test that SPRY3 normalizes to correct gene concept."""
# Concept ID
resp = ncbi.search('NCBIgene:10251')
check_resp_single_record(resp, spry3, MatchType.CONCEPT_ID)
# Symbol
resp = ncbi.search('sprY3')
check_resp_single_record(resp, spry3, MatchType.SYMBOL)
# Alias
resp = ncbi.search('SPRY-3')
check_resp_single_record(resp, spry3, MatchType.ALIAS)
def test_tp53(tp53, hgnc):
"""Test that tp53 normalizes to correct gene concept."""
# Concept ID
resp = hgnc.search('hgnc:11998')
check_resp_single_record(resp, tp53, MatchType.CONCEPT_ID)
resp = hgnc.search('HGNC:11998')
check_resp_single_record(resp, tp53, MatchType.CONCEPT_ID)
resp = hgnc.search('Hgnc:11998')
check_resp_single_record(resp, tp53, MatchType.CONCEPT_ID)
# Symbol
resp = hgnc.search('tp53')
check_resp_single_record(resp, tp53, MatchType.SYMBOL)
resp = hgnc.search('TP53')
check_resp_single_record(resp, tp53, MatchType.SYMBOL)
# Alias
resp = hgnc.search('LFS1')
check_resp_single_record(resp, tp53, MatchType.ALIAS)
resp = hgnc.search('p53')
check_resp_single_record(resp, tp53, MatchType.ALIAS)
