def load_kmer_model(filename):
with h5py.File(filename, "r") as file:
central_position = file.attrs["central_pos"]
model_table = file["model"]
mean = np.zeros(len(model_table))
sigma = np.zeros(len(model_table))
k = None
for line in model_table:
kmer = line[0].decode("ascii")
kmer_id = kmer_to_id(kmer)
mean[kmer_id] = line[1]
sigma[kmer_id] = line[2]
k = len(kmer)
return KmerModel(k, central_position, len(alphabet), mean, sigma)
X.append(x)
Y.append(y)
return X, Y
################################################################################
posReadsPaths = getReadsInFolder(readsPosFilePath, minSize=0)
negReadsPaths = getReadsInFolder(readsNegFilePath, minSize=0)
index = getAlignedIndex(alignedSquiggles)
ref = Fasta(refFilePath)
# load basecalled sequence and signal
mod = KmerModel.load_from_hdf5(kmerModelFilePath)
################################################################################
pomery = [[[] for j in kmerLen] for i in levels]
overlap = [[[] for j in kmerLen] for i in levels]
goodDash = [[] for i in levels]
badDash = [[] for i in levels]
alignLenRead = [0 for _ in levels]
alignLenFake = [0 for _ in levels]
longestCommonK = [[0 for j in kmerLen] for i in levels]
readCounter = 0
for posRead in posReadsPaths:
if readCounter == readNum:
break