lambertsbennett/gohencode

One-hot encoding of biological sequence data in Go.

GOHencode

One-hot encoding of biological sequence data in Go.

Premise

Many common neural network architectures can accept one-hot encoded data as input. GOHencode is a convenient tool to one-hot encode entire fasta files.

The input to GOHencode is a (gzipped) fasta file of sequences. These files have a structure as follows:

>Sequence-identifier
ATCGAA

GOHencode processes a fasta file and returns a parquet file with the following structure:

Sequence ID	Encoded Sequence Array
Sequence identifier 1	[4*len(sequence)]

The encoded sequence array has the following form for the sample sequence above:

A | 1 | 0 | 0 | 0 | 1 | 1  
C | 0 | 0 | 1 | 0 | 0 | 0  
T | 0 | 1 | 0 | 0 | 0 | 0  
G | 0 | 0 | 0 | 1 | 0 | 0  

The one-hot encoded output is stored as a parquet file with the form:

Base1	Base2	...	Basen
[1 0 0 0]	[0 0 1 0]	...	[...]