gtnet.sequence module

class gtnet.sequence.FastaSequenceEncoder(window, step, vocab=None, padval=None, min_seq_len=100, device=device(type='cpu'))

Bases: object

encode(seq)

classmethod get_dna_map(vocab=None)

Create data structures for mapping DNA sequence to

Returns

vocab: the DNA vocabulary used for building the data structures basemap: a 128 element array for mapping ASCII character values to encoded values rcmap: an array for mapping between complementary characters of encoded values

classmethod get_revcomp_map(vocab)

class gtnet.sequence.FastaReader(encoder, *fastas, parallel=False)

Bases: Process