def test_string_kernel():
mutations = numpy.eye( 4, dtype = numpy.float64 )
c = string_kernel.MismatchKernelCalculator.create( mutations )
seqs = string_kernel.convert_to_sequence_vec(
[
[ 1, 1, 2, 3 ],
[ 0, 1, 2, 3 ],
[ 0, 1, 2, 3 ],
[ 2, 1, 2, 2 ],
]
)
k = c.calculate( seqs )
# print k
strings = [
'a',
't',
'a',
''
]
k, sym_to_idx, idx_to_sym = string_kernel.mismatch_kernel( strings, mismatch_weight )
print k
print sym_to_idx
print idx_to_sym
class SubMatWeight( object ):
def __init__( self, sub_mat ):
self.sub_mat = sub_mat
def __call__( self, a, b ):
k = a < b and (a,b) or (b,a)
if not self.sub_mat.has_key( k ):
raise RuntimeError(
'Substitution matrix does not have key: %s' % str( k )
)
return self.sub_mat[ k ]
k, sym_to_idx, idx_to_sym = string_kernel.mismatch_kernel(
[
'ABCDEFGHIKLMNPQRSTVWXYZ',
'AAAE',
'ABCDEFGHIKLMNPQRSTVWXYZ',
],
SubMatWeight( sub_mat )
)
def load_scop(
scop_data_dir = 'c:/data/scop',
scop_version = '1.71'
):
"""Return the entire scop hierachy parsed from the data files"""
import corebio.resource.scop
return corebio.resource.scop.Scop.parse_files(
cla_file = open( '%s/dir.cla.scop.txt_%s' % (scop_data_dir, scop_version), 'r' ),
des_file = open( '%s/dir.des.scop.txt_%s' % (scop_data_dir, scop_version), 'r' ),
hie_file = open( '%s/dir.hie.scop.txt_%s' % (scop_data_dir, scop_version), 'r' )
)
