def test_read_blosum(self): f = data.data_stream("blosum80") mat = SubMatrix.read(f) self.assertEqual(mat[0, 10], -3) f.close() f = data.data_stream("blosum62") mat = SubMatrix.read(f) self.assertEqual(mat[4, 5], -4) f.close()
def test_read_pam(self): f = data.data_stream("pam250") mat = SubMatrix.read(f) self.assertEqual(mat[0, 0], 2.0) f.close() f = data.data_stream("pam120") mat = SubMatrix.read(f) self.assertEqual(mat[4, 5], -7) f.close()
def _build_default_registry() : registry = dict() # Parse database specifications from standard 'dbxref' file. ds = _read_dbxref( data_stream('dbxref.txt') ) ds.append(DataSource( name= 'Swiss-Prot', abbrev = 'swissprot', alt_abbrev = ('uniprotkb', 'uniprot'), url = 'http://ca.expasy.org/sprot/', resource_url = 'http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?%s', description='Protein knowledgebase', ) ) for d in ds : registry[d.abbrev.lower() ] = d if d.alt_abbrev : for alt in d.alt_abbrev : registry[alt.lower()] = ds return registry
def _build_default_registry(): registry = dict() # Parse database specifications from standard 'dbxref' file. ds = _read_dbxref(data_stream('dbxref.txt')) ds.append( DataSource( name='Swiss-Prot', abbrev='swissprot', alt_abbrev=('uniprotkb', 'uniprot'), url='http://ca.expasy.org/sprot/', resource_url='http://www.expasy.ch/cgi-bin/get-sprot-raw.pl?%s', description='Protein knowledgebase', )) for d in ds: registry[d.abbrev.lower()] = d if d.alt_abbrev: for alt in d.alt_abbrev: registry[alt.lower()] = ds return registry
def test_read_blosum(self): mat = SubMatrix.read( data.data_stream("blosum80") ) self.assertEquals(mat[0,10], -3) mat = SubMatrix.read( data.data_stream("blosum62") ) self.assertEquals(mat[4,5], -4)
def test_read_pam(self): mat = SubMatrix.read( data.data_stream("pam250") ) self.assertEquals(mat[0,0], 2.0) mat = SubMatrix.read( data.data_stream("pam120") ) self.assertEquals(mat[4,5], -7)