Make a generator that can create a tensor with the following dimensions (genome region, frag. length, end sequences).
The sequences should be found in the in the reference genome.
In order to store the sequences as counts, create a mapping from seq string to a base 4 string where the nucleotide having the following values
A -> 0
T -> 1
G -> 2
C -> 3
The index in the tensor is then the conversion from base 4 to base 10.
Hogfeldt
commented
4 years ago
Make a generator that can create a tensor with the following dimensions (genome region, frag. length, end sequences). The sequences should be found in the in the reference genome. In order to store the sequences as counts, create a mapping from seq string to a base 4 string where the nucleotide having the following values A -> 0 T -> 1 G -> 2 C -> 3 The index in the tensor is then the conversion from base 4 to base 10.