How to convert DNA sequences in FASTA format to OneHot Encoded Pandas Dataframe for Neural Networks?

Question

DNA sequences in FASTA format look like:
CATGCATTAGTTATTAATAGTAATCAATTACGGGGTCATTAGTTCA...

I am trying to convert them into one-hot encoded data in a Pandas dataframe so that I can use various neural networks to analyze them. This has probably been done many times. Can someone point me to references or Python packages for it?

prashant0598 · Accepted Answer

I am not sure about any python package but you can simply do integer encoding using labelencoder() and then do one-hot encoding.
label_encoder = LabelEncoder()
integer_encoded_seq = label_encoder.fit_transform(seq)    
onehot_encoder = OneHotEncoder(sparse=False)
integer_encoded_seq = integer_encoded_seq.reshape(len(integer_encoded_seq), 1)
onehot_encoded_seq = onehot_encoder.fit_transform(integer_encoded_seq)

Refer this.

How to convert DNA sequences in FASTA format to OneHot Encoded Pandas Dataframe for Neural Networks?

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