def __init__(self, seqs):
        self._seqs = list(seqs)

        self._seq_lens = np.array([len(seq) for seq in self._seqs])
        assert self._seq_lens.max() == self._seq_lens.min()
        self.seq_len = self._seq_lens[0]

        self.one_hot_coded_seqs = one_hot_encode_sequences(self._seqs)
        self.freq_one_hot_coded_seqs = self._init_freq_one_hot_coded_seqs()
Exemple #2
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    def __init__(self, seqs, include_shape=True):
        self._seqs = list(seqs)

        self._seq_lens = np.array([len(seq) for seq in self._seqs])
        assert self._seq_lens.max() == self._seq_lens.min()
        self.seq_len = self._seq_lens[0]

        self.fwd_one_hot_coded_seqs = one_hot_encode_sequences(self._seqs)
        self.rc_one_hot_coded_seqs = self.fwd_one_hot_coded_seqs[:,::-1,::-1]
        
        if include_shape:
            (self.fwd_shape_features, self.rc_shape_features 
            ) = code_seqs_shape_features(
                self._seqs, self.seq_len, len(self._seqs))

            self.fwd_coded_seqs = np.dstack(
                (self.fwd_one_hot_coded_seqs, self.fwd_shape_features))
            self.rc_coded_seqs = np.dstack(
                (self.rc_one_hot_coded_seqs, self.rc_shape_features))
        else:
            self.fwd_shape_features, self.rc_shape_features = None, None
            self.fwd_coded_seqs = self.fwd_one_hot_coded_seqs
            self.rc_coded_seqs = self.rc_one_hot_coded_seqs