def test_tau_sites():
pm = ProtMapper()
ms = pm.map_to_human_ref('P10636', 'uniprot', 'S', '320')
assert isinstance(ms, MappedSite)
assert ms == MappedSite(up_id='P10636',
error_code=None,
valid=False,
orig_res='S',
orig_pos='320',
mapped_id='P10636',
mapped_res='S',
mapped_pos='637',
description='position from isoform 8',
gene_name='MAPT'), ms
ms = pm.map_to_human_ref('P10636', 'uniprot', 'T', '153')
assert isinstance(ms, MappedSite)
assert ms == MappedSite(up_id='P10636',
error_code=None,
valid=False,
orig_res='T',
orig_pos='153',
mapped_id='P10636-8',
mapped_res='T',
mapped_pos='153',
description='INFERRED_ALTERNATIVE_ISOFORM',
gene_name='MAPT'), ms
def test_check_agent_mod_up_id():
sm = ProtMapper()
ms = sm.map_to_human_ref('P28482', 'uniprot', 'T', '185')
assert ms == MappedSite(up_id='P28482',
error_code=None,
valid=True,
orig_res='T',
orig_pos='185',
mapped_id=None,
mapped_res=None,
mapped_pos=None,
description='VALID',
gene_name='MAPK1')
assert ms.not_invalid() is True
assert ms.has_mapping() is False
ms = sm.map_to_human_ref('P28482', 'uniprot', 'T', '183')
assert ms == MappedSite(up_id='P28482',
error_code=None,
valid=False,
orig_res='T',
orig_pos='183',
mapped_id='P28482',
mapped_res='T',
mapped_pos='185',
description='INFERRED_MOUSE_SITE',
gene_name='MAPK1')
assert ms.not_invalid() is False
assert ms.has_mapping() is True
def test_map_from_sitemap():
sm = ProtMapper()
ms = sm.map_to_human_ref('P15056', 'uniprot', 'S', '753')
assert ms == MappedSite(up_id='P15056', valid=False, orig_res='S',
orig_pos='753', mapped_id='P15056',
mapped_res='T', mapped_pos='753',
description='wrong residue', gene_name='BRAF')
def test_map_rat_site():
sm = ProtMapper()
ms = sm.map_to_human_ref('NPHS1', 'hgnc', 'Y', '1204')
assert ms == MappedSite(up_id='O60500', error_code=None, valid=False,
orig_res='Y', orig_pos='1204', mapped_id='O60500',
mapped_res='Y', mapped_pos='1193',
description='INFERRED_RAT_SITE', gene_name='NPHS1')
def test_check_agent_mod_hgnc():
sm = ProtMapper()
ms = sm.map_to_human_ref('MAPK1', 'hgnc', 'T', '185')
assert ms == MappedSite(up_id='P28482',
error_code=None,
valid=True,
orig_res='T',
orig_pos='185',
mapped_id=None,
mapped_res=None,
mapped_pos=None,
description='VALID',
gene_name='MAPK1')
ms = sm.map_to_human_ref('MAPK1', 'hgnc', 'T', '183')
assert ms == MappedSite(up_id='P28482',
error_code=None,
valid=False,
orig_res='T',
orig_pos='183',
mapped_id='P28482',
mapped_res='T',
mapped_pos='185',
description='INFERRED_MOUSE_SITE',
gene_name='MAPK1')
def test_set_s9():
pm = ProtMapper()
ms = pm.map_to_human_ref('Q01105', 'uniprot', 'S', '9')
assert ms == MappedSite(up_id='Q01105', valid=False, orig_res='S',
orig_pos='9', mapped_id='Q01105-2',
mapped_res='S', mapped_pos='9',
description='INFERRED_ALTERNATIVE_ISOFORM',
gene_name='SET'), ms
def test_smpd1_s508():
pm = ProtMapper()
ms = pm.map_to_human_ref('P17405', 'uniprot', 'S', '508')
assert ms == MappedSite(up_id='P17405', valid=False, orig_res='S',
orig_pos='508', mapped_id='P17405',
mapped_res='S', mapped_pos='510',
description='REMAPPED_FROM_PSP_SEQUENCE',
gene_name='SMPD1')
def test_myl9_s19():
pm = ProtMapper()
ms = pm.map_to_human_ref('P24844', 'uniprot', 'S', '19')
assert ms == MappedSite(up_id='P24844', error_code=None, valid=False,
orig_res='S', orig_pos='19', mapped_id='P24844',
mapped_res='S', mapped_pos='20',
description='INFERRED_METHIONINE_CLEAVAGE',
gene_name='MYL9')
def test_h2afx_s139():
pm = ProtMapper()
ms = pm.map_to_human_ref('P16104', 'uniprot', 'S', '139')
assert ms == MappedSite(up_id='P16104', valid=False, orig_res='S',
orig_pos='139', mapped_id='P16104',
mapped_res='S', mapped_pos='140',
description='REMAPPED_FROM_PSP_SEQUENCE',
gene_name='H2AFX')
def test_map_invalid_from_sitemap():
sm = ProtMapper()
ms = sm.map_to_human_ref('P06400', 'uniprot', 'D', '1')
assert ms == MappedSite(up_id='P06400', valid=False, orig_res='D',
orig_pos='1', mapped_id='P06400',
mapped_res=None, mapped_pos=None,
description='probable reading error: cyclin D1',
gene_name='RB1')
def test_map_methionine_cleavage():
sm = ProtMapper()
ms = sm.map_to_human_ref('DAXX', 'hgnc', 'S', '667')
assert ms == MappedSite(up_id='Q9UER7', error_code=None, valid=False,
orig_res='S', orig_pos='667', mapped_id='Q9UER7',
mapped_res='S', mapped_pos='668',
description='INFERRED_METHIONINE_CLEAVAGE',
gene_name='DAXX')
def test_map_mouse_site():
sm = ProtMapper()
ms = sm.map_to_human_ref('THEMIS2', 'hgnc', 'Y', '660')
assert ms == MappedSite(up_id='Q5TEJ8', error_code=None, valid=False,
orig_res='Y', orig_pos='660', mapped_id='Q5TEJ8',
mapped_res='Y',
mapped_pos='632', description='INFERRED_MOUSE_SITE',
gene_name='THEMIS2')
def test_egfr_mouse_1068_to_human_1092():
pm = ProtMapper()
ms = pm.map_to_human_ref('Q01279', 'uniprot', 'Y', '1068')
assert ms == MappedSite(up_id='Q01279', error_code=None, valid=False,
orig_res='Y', orig_pos='1068', mapped_id='P00533',
mapped_res='Y', mapped_pos='1092',
description='SIGNAL_PEPTIDE_REMOVED',
gene_name='Egfr')
def test_invalid_gene_name_error():
sm = ProtMapper()
ms = sm.map_to_human_ref('ASDF', 'hgnc', 'Q', '999')
assert ms.error_code == 'NO_UNIPROT_ID'
assert ms == MappedSite(up_id=None, error_code='NO_UNIPROT_ID',
valid=None, orig_res='Q', orig_pos='999', mapped_id=None,
mapped_res=None, mapped_pos=None, description=None,
gene_name='ASDF')
def test_map_invalid_residue():
pm = ProtMapper()
ms = pm.map_to_human_ref('MAPK1', 'hgnc', 'B', '185')
assert ms == MappedSite('P28482', None, 'B', '185',
error_code='INVALID_SITE',
description='Residue B not a valid amino acid')
assert ms.not_invalid() is True
assert ms.has_mapping() is False
def test_repr_str():
sm = ProtMapper()
ms = sm.map_to_human_ref('MAPK1', 'hgnc', 'T', '183')
assert str(ms) == ("MappedSite(up_id='P28482', error_code=None, "
"valid=False, orig_res='T', orig_pos='183', "
"mapped_id='P28482', "
"mapped_res='T', mapped_pos='185', "
"description='INFERRED_MOUSE_SITE', "
"gene_name='MAPK1')")
def test_signal_peptide():
pm = ProtMapper()
ms = pm.map_to_human_ref('P04626', 'uniprot', 'Y', '1226')
assert isinstance(ms, MappedSite)
assert ms == MappedSite(up_id='P04626', error_code=None, valid=False,
orig_res='Y', orig_pos='1226', mapped_id='P04626',
mapped_res='Y', mapped_pos='1248',
description='SIGNAL_PEPTIDE_REMOVED',
gene_name='ERBB2'), ms
def test_map_invalid_position2():
pm = ProtMapper()
ms = pm.map_to_human_ref('MAPK1', 'hgnc', 'T', '12.5')
assert ms == MappedSite(
'P28482',
None,
'T',
'12.5',
error_code='INVALID_SITE',
description='Position 12.5 not a valid sequence position.')
def test_map_peptide():
sm = ProtMapper()
# Check the localization of a peptide to a target protein
peptide = 'MNTPSQPRQHFY'
pos = 5
respos = sm.map_peptide('Q04637-1', peptide, pos)
assert respos == 45
# Check that the motif is not found in an unrelated sequence
respos = sm.map_peptide('O95218-2', peptide, pos)
assert respos is None
def test_peptide_round_trip():
pm = ProtMapper()
pos = '187'
motif, site_pos = pm.motif_from_position('P28482', '187')
ms = pm.map_peptide_to_human_ref('MAPK1', 'hgnc', motif, site_pos)
assert isinstance(ms, MappedSite)
assert ms == MappedSite(up_id='P28482', error_code=None, valid=True,
orig_res=None, orig_pos=None, mapped_id='P28482',
mapped_res='Y', mapped_pos='187',
description=None, gene_name='MAPK1')
def test_invalid_uniprot_http_error():
"""Trigger an HTTP Error by passing in an invalid Uniprot ID. The error
should be indicated in the returned MappedSite."""
sm = ProtMapper()
ms = sm.map_to_human_ref('ASDF', 'uniprot', 'Q', '999')
assert ms.error_code == 'UNIPROT_HTTP_NOT_FOUND'
assert ms == MappedSite(up_id='ASDF', error_code='UNIPROT_HTTP_NOT_FOUND',
valid=None, orig_res='Q', orig_pos='999',
mapped_id=None, mapped_res=None, mapped_pos=None,
description=None, gene_name=None)
def test_manual_vs_methionine():
# Make sure the manual mapping for EGFR 1068 is used instead of the
# methionine off-by-one mapping
pm = ProtMapper()
ms = pm.map_to_human_ref('P00533', 'uniprot', 'Y', '1068')
assert isinstance(ms, MappedSite)
assert ms == MappedSite(up_id='P00533', error_code=None, valid=False,
orig_res='Y', orig_pos='1068', mapped_id='P00533',
mapped_res='Y', mapped_pos='1092',
description='numbering after 24-residue signaling peptide removed',
gene_name='EGFR')
def test_map_peptide_to_human_ref2():
pm = ProtMapper()
up_id = 'P07942'
peptide = 'GDNLLDSRMEIRE'
sitepos = 7
ms = pm.map_peptide_to_human_ref(up_id, 'uniprot', peptide, sitepos)
assert ms == MappedSite(up_id='P07942', error_code=None, valid=True,
orig_res=None, orig_pos=None, mapped_id='P07942',
mapped_res='S', mapped_pos='250', description=None,
gene_name='LAMB1')
assert ms
def test_map_peptide_to_human_ref():
sm = ProtMapper()
peptide = 'MNTPSQPRQHFY'
pos = 5
ms = sm.map_peptide_to_human_ref('Q04637', 'uniprot', peptide, pos)
assert isinstance(ms, MappedSite)
assert ms == MappedSite(up_id='Q04637', error_code=None, valid=True,
orig_res=None, orig_pos=None, mapped_id='Q04637',
mapped_res='S', mapped_pos='45',
description=None, gene_name='EIF4G1')
# The same as above except with the gene name instead
ms2 = sm.map_peptide_to_human_ref('EIF4G1', 'hgnc', peptide, pos)
assert ms2 == ms
def test_motif_from_position():
sm = ProtMapper()
# Try with string position
(motif, respos) = sm.motif_from_position('O95218-2', '120', window=7)
assert motif == 'EYIEREESDGEYDEF'
assert respos == 8
# Also try with int
motif, respos = sm.motif_from_position('O95218-2', '120')
assert motif == 'EYIEREESDGEYDEF'
assert respos == 8
# Change the window size
motif, respos = sm.motif_from_position('O95218-2', '120', window=5)
assert motif == 'IEREESDGEYD'
assert respos == 6
# Try with a residue that is close to the end of the protein
motif, respos = sm.motif_from_position('Q04637-1', '1596', window=7)
assert motif == 'LREAEEESDHN'
assert respos == 8
# Try with a residue that is close to the start of the protein
motif, respos = sm.motif_from_position('Q04637-1', '3', window=7)
assert motif == 'MNKAPQSTGP'
assert respos == 3
(motif, respos) = sm.motif_from_position('P28482', '187')
assert motif == 'HTGFLTEYVATRWYR'
assert respos == 8
def test_write_cache():
cache_path = join(dirname(abspath(__file__)), 'test_cache_write.pkl')
assert not isfile(cache_path)
sm = ProtMapper(use_cache=True, cache_path=cache_path)
ms = sm.map_to_human_ref('P28482', 'uniprot', 'T', '183')
del sm
assert isfile(cache_path)
with open(cache_path, 'rb') as f:
cache_dict = pickle.load(f)
assert isinstance(cache_dict, dict)
assert len(cache_dict) == 1
ms = cache_dict[('P28482', 'T', '183')]
assert ms == MappedSite(up_id='P28482', error_code=None, valid=False,
orig_res='T', orig_pos='183', mapped_id='P28482',
mapped_res='T', mapped_pos='185',
description='INFERRED_MOUSE_SITE',
gene_name='MAPK1')
os.unlink(cache_path)
def test_mutliple_up_ids():
up_id = _get_uniprot_id('TMPO', 'hgnc')
assert up_id == 'P42166'
pm = ProtMapper()
ms = pm.map_peptide_to_human_ref('TMPO', 'hgnc', 'RKVPRLSEKSVEE', 7)
assert ms.up_id == 'P42166'
def test_invalid_prot_ns():
sm = ProtMapper()
sm.map_to_human_ref('MAPK1', 'hgncsymb', 'T', '185')
def test_signal_peptide_no_error():
pm = ProtMapper()
ms = pm.map_to_human_ref('Q9RI12', 'uniprot', 'S', '38')
