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'