def setUp(self):
self.registry = MiniRegistry()
>>> s = DNA('GG-GG')
>>> for motif_slice in s.find_motifs('purine-run', ignore=s.gaps()):
... motif_slice
slice(0, 5, None)
"""
if motif_type not in self._motifs:
raise ValueError("Not a known motif (%r) for this sequence (%s)." %
(motif_type, self.__class__.__name__))
return self._motifs[motif_type](self, min_length, ignore)
@overrides(Sequence)
def _constructor(self, **kwargs):
return self.__class__(validate=False, lowercase=False, **kwargs)
@overrides(Sequence)
def _repr_stats(self):
"""Define custom statistics to display in the sequence's repr."""
stats = super(GrammaredSequence, self)._repr_stats()
stats.append(('has gaps', '%r' % self.has_gaps()))
stats.append(('has degenerates', '%r' % self.has_degenerates()))
stats.append(('has definites', '%r' % self.has_definites()))
return stats
_motifs = MiniRegistry()
# Leave this at the bottom
_motifs.interpolate(GrammaredSequence, "find_motifs")
