% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/generators.R
\name{get_generator}
\alias{get_generator}
\title{Wrapper for generator functions}
\usage{
get_generator(
  path = NULL,
  train_type,
  batch_size,
  maxlen,
  step = NULL,
  shuffle_file_order = FALSE,
  vocabulary = c("A", "C", "G", "T"),
  seed = 1,
  proportion_entries = NULL,
  shuffle_input = FALSE,
  format = "fasta",
  path_file_log = NULL,
  reverse_complement = FALSE,
  n_gram = NULL,
  n_gram_stride = NULL,
  output_format = "target_right",
  ambiguous_nuc = "zero",
  proportion_per_seq = NULL,
  skip_amb_nuc = NULL,
  use_quality_score = FALSE,
  padding = FALSE,
  added_label_path = NULL,
  target_from_csv = NULL,
  add_input_as_seq = NULL,
  max_samples = NULL,
  concat_seq = NULL,
  target_len = 1,
  file_filter = NULL,
  use_coverage = NULL,
  sample_by_file_size = FALSE,
  add_noise = NULL,
  random_sampling = FALSE,
  set_learning = NULL,
  file_limit = NULL,
  reverse_complement_encoding = FALSE,
  read_data = FALSE,
  target_split = NULL,
  path_file_logVal = NULL,
  model = NULL,
  vocabulary_label = NULL,
  masked_lm = NULL,
  val = FALSE,
  return_int = FALSE,
  verbose = TRUE,
  delete_used_files = FALSE,
  reshape_xy = NULL
)
}
\arguments{
\item{path}{Path to training data. If \code{train_type} is \code{label_folder}, should be a vector or list
where each entry corresponds to a class (list elements can be directories and/or individual files). If \code{train_type} is not \code{label_folder},
can be a single directory or file or a list of directories and/or files.}

\item{train_type}{Either \code{"lm"}, \code{"lm_rds"}, \code{"masked_lm"} for language model; \code{"label_header"}, \code{"label_folder"}, \code{"label_csv"}, \code{"label_rds"} for classification or \code{"dummy_gen"}.
\itemize{
\item Language model is trained to predict character(s) in a sequence. \cr
\item \code{"label_header"}/\code{"label_folder"}/\code{"label_csv"} are trained to predict a corresponding class given a sequence as input.
\item If \code{"label_header"}, class will be read from fasta headers.
\item If \code{"label_folder"}, class will be read from folder, i.e. all files in one folder must belong to the same class.
\item If \code{"label_csv"}, targets are read from a csv file. This file should have one column named "file". The targets then correspond to entries in that row (except "file"
column). Example: if we are currently working with a file called "a.fasta" and corresponding label is "label_1", there should be a row in our csv file\tabular{lll}{
   file \tab label_1 \tab label_2 \cr
   "a.fasta" \tab 1 \tab 0 \cr
}


\item If \code{"label_rds"}, generator will iterate over set of .rds files containing each a list of input and target tensors. Not implemented for model
with multiple inputs.
\item If \code{"lm_rds"}, generator will iterate over set of .rds files and will split tensor according to \code{target_len} argument
(targets are last \code{target_len} nucleotides of each sequence).
\item  If \code{"dummy_gen"}, generator creates random data once and repeatedly feeds these to model.
\item  If \code{"masked_lm"}, generator maskes some parts of the input. See \code{masked_lm} argument for details.
}}

\item{batch_size}{Number of samples used for one network update.}

\item{maxlen}{Length of predictor sequence.}

\item{step}{Frequency of sampling steps.}

\item{shuffle_file_order}{Boolean, whether to go through files sequentially or shuffle beforehand.}

\item{vocabulary}{Vector of allowed characters. Characters outside vocabulary get encoded as specified in \code{ambiguous_nuc}.}

\item{seed}{Sets seed for reproducible results.}

\item{proportion_entries}{Proportion of fasta entries to keep. For example, if fasta file has 50 entries and \code{proportion_entries = 0.1},
will randomly select 5 entries.}

\item{shuffle_input}{Whether to shuffle entries in file.}

\item{format}{File format, \code{"fasta"}, \code{"fastq"}, \code{"rds"} or \code{"fasta.tar.gz"}, \code{"fastq.tar.gz"} for \code{tar.gz} files.}

\item{path_file_log}{Write name of files used for training to csv file if path is specified.}

\item{reverse_complement}{Boolean, for every new file decide randomly to use original data or its reverse complement.}

\item{n_gram}{Integer, encode target not nucleotide wise but combine n nucleotides at once. For example for \verb{n=2, "AA" ->  (1, 0,..., 0),}
\verb{"AC" ->  (0, 1, 0,..., 0), "TT" -> (0,..., 0, 1)}, where the one-hot vectors have length \code{length(vocabulary)^n}.}

\item{n_gram_stride}{Step size for n-gram encoding. For AACCGGTT with \code{n_gram = 4} and \code{n_gram_stride = 2}, generator encodes
\verb{(AACC), (CCGG), (GGTT)}; for \code{n_gram_stride = 4} generator encodes \verb{(AACC), (GGTT)}.}

\item{output_format}{Determines shape of output tensor for language model.
Either \code{"target_right"}, \code{"target_middle_lstm"}, \code{"target_middle_cnn"} or \code{"wavenet"}.
Assume a sequence \code{"AACCGTA"}. Output correspond as follows
\itemize{
\item \verb{"target_right": X = "AACCGT", Y = "A"}
\item \verb{"target_middle_lstm": X = (X_1 = "AAC", X_2 = "ATG"), Y = "C"} (note reversed order of X_2)
\item \verb{"target_middle_cnn": X = "AACGTA", Y = "C"}
\item \verb{"wavenet": X = "AACCGT", Y = "ACCGTA"}
}}

\item{ambiguous_nuc}{How to handle nucleotides outside vocabulary, either \code{"zero"}, \code{"discard"}, \code{"empirical"} or \code{"equal"}.
\itemize{
\item If \code{"zero"}, input gets encoded as zero vector.
\item If \code{"equal"}, input is repetition of \code{1/length(vocabulary)}.
\item If \code{"discard"}, samples containing nucleotides outside vocabulary get discarded.
\item If \code{"empirical"}, use nucleotide distribution of current file.
}}

\item{proportion_per_seq}{Numerical value between 0 and 1. Proportion of sequence to take samples from (use random subsequence).}

\item{skip_amb_nuc}{Threshold of ambiguous nucleotides to accept in fasta entry. Complete entry will get discarded otherwise.}

\item{use_quality_score}{Whether to use fastq quality scores. If \code{TRUE} input is not one-hot-encoding but corresponds to probabilities.
For example (0.97, 0.01, 0.01, 0.01) instead of (1, 0, 0, 0).}

\item{padding}{Whether to pad sequences too short for one sample with zeros.}

\item{added_label_path}{Path to file with additional input labels. Should be a csv file with one column named "file". Other columns should correspond to labels.}

\item{target_from_csv}{Path to csv file with target mapping. One column should be called "file" and other entries in row are the targets.}

\item{add_input_as_seq}{Boolean vector specifying for each entry in \code{added_label_path} if rows from csv should be encoded as a sequence or used directly.
If a row in your csv file is a sequence this should be \code{TRUE}. For example you may want to add another sequence, say ACCGT. Then this would correspond to 1,2,2,3,4 in
csv file (if vocabulary = c("A", "C", "G", "T")).  If \code{add_input_as_seq} is \code{TRUE}, 12234 gets one-hot encoded, so added input is a 3D tensor.  If \code{add_input_as_seq} is
\code{FALSE} this will feed network just raw data (a 2D tensor).}

\item{max_samples}{Maximum number of samples to use from one file. If not \code{NULL} and file has more than \code{max_samples} samples, will randomly choose a
subset of \code{max_samples} samples.}

\item{concat_seq}{Character string or \code{NULL}. If not \code{NULL} all entries from file get concatenated to one sequence with \code{concat_seq} string between them.
Example: If 1.entry AACC, 2. entry TTTG and \code{concat_seq = "ZZZ"} this becomes AACCZZZTTTG.}

\item{target_len}{Number of nucleotides to predict at once for language model.}

\item{file_filter}{Vector of file names to use from path_corpus.}

\item{use_coverage}{Integer or \code{NULL}. If not \code{NULL}, use coverage as encoding rather than one-hot encoding and normalize.
Coverage information must be contained in fasta header: there must be a string \code{"cov_n"} in the header, where \code{n} is some integer.}

\item{sample_by_file_size}{Sample new file weighted by file size (bigger files more likely).}

\item{add_noise}{\code{NULL} or list of arguments. If not \code{NULL}, list must contain the following arguments: \code{noise_type} can be \code{"normal"} or \code{"uniform"};
optional arguments \code{sd} or \code{mean} if noise_type is \code{"normal"} (default is \code{sd=1} and \code{mean=0}) or \verb{min, max} if \code{noise_type} is \code{"uniform"}
(default is \verb{min=0, max=1}).}

\item{random_sampling}{Whether samples should be taken from random positions when using \code{max_samples} argument. If \code{FALSE} random
samples are taken from a consecutive subsequence.}

\item{set_learning}{When you want to assign one label to set of samples. Only implemented for \code{train_type = "label_folder"}.
Input is a list with the following parameters
\itemize{
\item \code{samples_per_target}: how many samples to use for one target.
\item \code{maxlen}: length of one sample.
\item \code{reshape_mode}: \verb{"time_dist", "multi_input"} or \code{"concat"}.
\itemize{
\item
If \code{reshape_mode} is \code{"multi_input"}, generator will produce \code{samples_per_target} separate inputs, each of length \code{maxlen} (model should have
\code{samples_per_target} input layers).
\item If reshape_mode is \code{"time_dist"}, generator will produce a 4D input array. The dimensions correspond to
\verb{(batch_size, samples_per_target, maxlen, length(vocabulary))}.
\item If \code{reshape_mode} is \code{"concat"}, generator will concatenate \code{samples_per_target} sequences
of length \code{maxlen} to one long sequence.
}
\item If \code{reshape_mode} is \code{"concat"}, there is an additional \code{buffer_len}
argument. If \code{buffer_len} is an integer, the subsequences are interspaced with \code{buffer_len} rows. The input length is
(\code{maxlen} \eqn{*} \code{samples_per_target}) + \code{buffer_len} \eqn{*} (\code{samples_per_target} - 1).
}}

\item{file_limit}{Integer or \code{NULL}. If integer, use only specified number of randomly sampled files for training. Ignored if greater than number of files in \code{path}.}

\item{reverse_complement_encoding}{Whether to use both original sequence and reverse complement as two input sequences.}

\item{read_data}{If \code{TRUE} the first element of output is a list of length 2, each containing one part of paired read. Maxlen should be 2*length of one read.}

\item{target_split}{If target gets read from csv file, list of names to divide target tensor into list of tensors.
Example: if csv file has header names \verb{"file", "label_1", "label_2", "label_3"} and \code{target_split = list(c("label_1", "label_2"), "label_3")},
this will divide target matrix to list of length 2, where the first element contains columns named \code{"label_1"} and \code{"label_2"} and the
second entry contains the column named \code{"label_3"}.}

\item{path_file_logVal}{Path to csv file logging used validation files.}

\item{model}{A keras model.}

\item{vocabulary_label}{Character vector of possible targets. Targets outside \code{vocabulary_label} will get discarded if
\code{train_type = "label_header"}.}

\item{masked_lm}{If not \code{NULL}, input and target are equal except some parts of the input are masked or random.
Must be list with the following arguments:
\itemize{
\item \code{mask_rate}: Rate of input to mask (rate of input to replace with mask token).
\item \code{random_rate}: Rate of input to set to random token.
\item \code{identity_rate}: Rate of input where sample weights are applied but input and output are identical.
\item \code{include_sw}: Whether to include sample weights.
\item \code{block_len} (optional): Masked/random/identity regions appear in blocks of size \code{block_len}.
}}

\item{val}{Logical, call initialized generator "genY" or "genValY" where Y is an integer between 1 and length of directories.}

\item{return_int}{Whether to return integer encoding or one-hot encoding.}

\item{verbose}{Whether to show messages.}

\item{delete_used_files}{Whether to delete file once used. Only applies for rds files.}

\item{reshape_xy}{Can be a list of functions to apply to input and/or target. List elements (containing the reshape functions)
must be called x for input or y for target and each have arguments called x and y. For example:
\code{reshape_xy = list(x = function(x, y) {return(x+1)}, y = function(x, y) {return(x+y)})} .
For rds generator needs to have an additional argument called sw.}
}
\value{
A generator function.
}
\description{
For a detailed description see the data generator \href{https://deepg.de/articles/data_generator.html}{tutorial}.
Will choose one of the generators from \code{\link{generator_fasta_lm}},
\code{\link{generator_fasta_label_folder}}, \code{\link{generator_fasta_label_header_csv}},
\code{\link{generator_rds}}, \code{\link{generator_random}}, \code{\link{generator_dummy}} or
\code{\link{generator_fasta_lm}} according to the \code{train_type} and \code{random_sampling}
arguments.
}
\examples{
\dontshow{if (reticulate::py_module_available("tensorflow")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
# create dummy fasta files
fasta_path <- tempfile()
dir.create(fasta_path)
create_dummy_data(file_path = fasta_path,
                  num_files = 3,
                  seq_length = 10,
                  num_seq = 5,
                  vocabulary = c("a", "c", "g", "t"))

gen <- get_generator(path = fasta_path,
                     maxlen = 5, train_type = "lm",
                     output_format = "target_right",
                     step = 3, batch_size = 7)
z <- gen()
x <- z[[1]]
y <- z[[2]]
dim(x)
dim(y)
\dontshow{\}) # examplesIf}
}