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_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_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_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'
