writeStatesByFastaEntries: Write states to h5 file
In hiddengenome/altum: deepG

writeStatesByFastaEntries Removes layers (optional) from pretrained model and calculates states of fasta file, writes a separate h5 file for every fasta entry in fasta file. h5 files also contain the nucleotide sequence and positions of targets corresponding to states. Names of output files are: file_path + "Nr" + i + filename + file_type, where i is the number of the fasta entry.

writeStatesByFastaEntries(
  model.path,
  layer.depth = NULL,
  fasta.path,
  round_digits = 2,
  file_name = "states.h5",
  file_path,
  step = 1,
  vocabulary = c("a", "c", "g", "t"),
  batch.size = 256,
  padding = FALSE,
  file_type = "h5",
  model = NULL,
  mode = "lm"
)

`model.path`	Path to a pretrained model.
`layer.depth`	Depth of layer to evaluate. If NULL last layer is used.
`fasta.path`	Path to fasta file.
`round_digits`	Number of decimal places.
`file_name`	Filename to store states, function adds "Nr" + "i" before name, where i is entry number.
`file_path`	Path to folder, where to write output.
`step`	Frequency of sampling steps.
`vocabulary`	Vector of allowed characters, character outside vocabulary get encoded as 0-vector.
`batch.size`	Number of samples to evaluate at once. Does not change output, only relevant for speed and memory.
`padding`	Logical scalar, generate states for first maxlen nucleotides by padding beginning of sequence with 0-vectors.
`file_type`	Either "h5" or "csv".
`model`	A keras model. If model and model.path are not NULL, model will be used for inference.
`mode`	Either "lm" for language model or "label" for label classification.
`seqStart`	Inserts character at beginning of sequence from one file.
`seqEnd`	Insert character at end of sequence from one file.
`withinFile`	Insert characters between fasta entries.