About Input Output File format

  • We provide utility code to read in FASTA string input format

    • See example data files @ Here

    • Also below we include two sequence examples in Fasta format

    • In each example’s header line: 1 represents positive class label and 0 represents negative class label (so the task is to classify a string into two classes)

>1
MKTPITEAIAAADNQGRFLSNTELQAVNGRYQRAAASLEAARSLTSNAERLINGAAQAVYSKFPYTSQMPGPQYASSAVGKAKCARDIGYYLRMVTYCLVVGGTGPMDEYLIAGLEEINRTFDLSPSWYVEALNYIKANHGLSGQAANEANTYIDYAINALS
>0
PYTINSPSQFVYLSSAYADPVELINLCTNALGNQFQTQQARTTVQQQFADAWKPSPVMTVRFPASDFYVYRYNSTLDPLITALLNSFDTRNRIIEVNNQPAPNTTEIVNATQRVDDATVAIRASINNLANELVRGTGMFNQAGFETASGLVWTTTPAT

  • However, the most basic input requriement for fastsk python functional call is just a simple numpy array; You can have whatever string format you prefer… and convert your format to numpy array…

Xtrain = [[1,0,1,0,1], [1,1,1,0,1]]
Xtest = [[1,1,1,1,1], [1,0,1,0,1]]

kernel.compute_kernel(Xtrain, Xtest)

train_kernel = kernel.get_train_kernel()
test_kernel = kernel.get_test_kernel()