R/generator_lm.R
In GenomeNet/deepG: Deep Learning for Genome Sequence Data
Defines functions
generator_fasta_lm
Documented in
generator_fasta_lm
#' Language model generator for fasta/fastq files
#'
#' @description Iterates over folder containing fasta/fastq files and produces encoding of predictor sequences
#' and target variables. Will take a sequence of fixed size and use some part of sequence as input and other part as target.
#'
#' @inheritParams train_model
#' @param path_corpus Input directory where fasta files are located or path to single file ending with fasta or fastq
#' (as specified in format argument). Can also be a list of directories and/or files.
#' @param format File format, either `"fasta"` or `"fastq"`.
#' @param batch_size Number of samples in one batch.
#' @param maxlen Length of predictor sequence.
#' @param max_iter Stop after `max_iter` number of iterations failed to produce a new batch.
#' @param shuffle_file_order Logical, whether to go through files randomly or sequentially.
#' @param step How often to take a sample.
#' @param seed Sets seed for `set.seed` function for reproducible results.
#' @param shuffle_input Whether to shuffle entries in every fasta/fastq file before extracting samples.
#' @param verbose Whether to show messages.
#' @param path_file_log Write name of files to csv file if path is specified.
#' @param reverse_complement Boolean, for every new file decide randomly to use original data or its reverse complement.
#' @param ambiguous_nuc How to handle nucleotides outside vocabulary, either `"zero"`, `"discard"`, `"empirical"` or `"equal"`.
#' \itemize{
#' \item If `"zero"`, input gets encoded as zero vector.
#' \item If `"equal"`, input is repetition of `1/length(vocabulary)`.
#' \item If `"discard"`, samples containing nucleotides outside vocabulary get discarded.
#' \item If `"empirical"`, use nucleotide distribution of current file.
#' }
#' @param proportion_per_seq Numerical value between 0 and 1. Proportion of sequence to take samples from (use random subsequence).
#' @param use_quality_score Whether to use fastq quality scores. If 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).
#' @param padding Whether to pad sequences too short for one sample with zeros.
#' @param 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.
#' @param 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 `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 `TRUE`, 12234 gets one-hot encoded, so added input is a 3D tensor. If \code{add_input_as_seq} is
#' `FALSE` this will feed network just raw data (a 2D tensor).
#' @param skip_amb_nuc Threshold of ambiguous nucleotides to accept in fasta entry. Complete entry will get discarded otherwise.
#' @param max_samples Maximum number of samples to use from one file. If not `NULL` and file has more than \code{max_samples} samples, will randomly choose a
#' subset of \code{max_samples} samples.
#' @param concat_seq Character string or `NULL`. If not `NULL` all entries from file get concatenated to one sequence with `concat_seq` string between them.
#' Example: If 1.entry AACC, 2. entry TTTG and `concat_seq = "ZZZ"` this becomes AACCZZZTTTG.
#' @param target_len Number of nucleotides to predict at once for language model.
#' @param file_filter Vector of file names to use from path_corpus.
#' @param use_coverage Integer or `NULL`. If not `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 `"cov_n"` in the header, where `n` is some integer.
#' @param proportion_entries Proportion of fasta entries to keep. For example, if fasta file has 50 entries and `proportion_entries = 0.1`,
#' will randomly select 5 entries.
#' @param sample_by_file_size Sample new file weighted by file size (bigger files more likely).
#' @param n_gram Integer, encode target not nucleotide wise but combine n nucleotides at once. For example for `n=2, "AA" -> (1, 0,..., 0),`
#' `"AC" -> (0, 1, 0,..., 0), "TT" -> (0,..., 0, 1)`, where the one-hot vectors have length `length(vocabulary)^n`.
#' @param add_noise `NULL` or list of arguments. If not `NULL`, list must contain the following arguments: \code{noise_type} can be `"normal"` or `"uniform"`;
#' optional arguments `sd` or `mean` if noise_type is `"normal"` (default is `sd=1` and `mean=0`) or `min, max` if `noise_type` is `"uniform"`
#' (default is `min=0, max=1`).
#' @param return_int Whether to return integer encoding or one-hot encoding.
#' @param 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:
#' `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.
#' @rawNamespace import(data.table, except = c(first, last, between))
#' @importFrom magrittr %>%
#' @examplesIf reticulate::py_module_available("tensorflow")
#' # create dummy fasta files
#' path_input_1 <- tempfile()
#' dir.create(path_input_1)
#' create_dummy_data(file_path = path_input_1,
#' num_files = 2,
#' seq_length = 8,
#' num_seq = 1,
#' vocabulary = c("a", "c", "g", "t"))
#'
#' gen <- generator_fasta_lm(path_corpus = path_input_1, batch_size = 2,
#' maxlen = 7)
#' z <- gen()
#' dim(z[[1]])
#' z[[2]]
#'
#' @returns A generator function.
#' @export
generator_fasta_lm <- function(path_corpus,
format = "fasta",
batch_size = 256,
maxlen = 250,
max_iter = 10000,
vocabulary = c("a", "c", "g", "t"),
verbose = FALSE,
shuffle_file_order = FALSE,
step = 1,
seed = 1234,
shuffle_input = FALSE,
file_limit = NULL,
path_file_log = NULL,
reverse_complement = FALSE,
output_format = "target_right",
ambiguous_nuc = "zeros",
use_quality_score = FALSE,
proportion_per_seq = NULL,
padding = TRUE,
added_label_path = NULL,
add_input_as_seq = NULL,
skip_amb_nuc = NULL,
max_samples = NULL,
concat_seq = NULL,
target_len = 1,
file_filter = NULL,
use_coverage = NULL,
proportion_entries = NULL,
sample_by_file_size = FALSE,
n_gram = NULL,
n_gram_stride = 1,
add_noise = NULL,
return_int = FALSE,
reshape_xy = NULL) {
##TODO: add check for n-gram and option for stride
# if (!is.null(n_gram) & !(any(n_gram_stride == c(n_gram, 1)))) {
# stop("When using language model with n_gram encoding, n_gram_stride must be 1 or equal to n_gram")
# }
if (!is.null(n_gram)) {
# maxlen_n_gram <- ceiling((maxlen - n_gram + 1)/n_gram_stride)
# target_len_n_gram <- ceiling((target_len - n_gram + 1)/n_gram_stride)
if (!n_gram_stride == n_gram) {
stop("When using train_type='lm' with n_gram encoding, n_gram_stride must be equal to n_gram.")
}
} # else {
# maxlen_n_gram <- maxlen
# target_len_n_gram <- target_len
# }
if (!is.null(reshape_xy)) {
reshape_xy_bool <- TRUE
reshape_x_bool <- ifelse(is.null(reshape_xy$x), FALSE, TRUE)
if (reshape_x_bool && !all(c('x', 'y') %in% formals(reshape_xy$x))) {
stop("function reshape_xy$x needs to have arguments named x and y")
}
reshape_y_bool <- ifelse(is.null(reshape_xy$y), FALSE, TRUE)
if (reshape_y_bool && !all(c('x', 'y') %in% formals(reshape_xy$y))) {
stop("function reshape_xy$y needs to have arguments named x and y")
}
} else {
reshape_xy_bool <- FALSE
}
total_seq_len <- maxlen + target_len
gen <- generator_fasta_label_folder(path_corpus = path_corpus,
format = format,
batch_size = batch_size,
maxlen = total_seq_len,
max_iter = max_iter,
vocabulary = vocabulary,
shuffle_file_order = shuffle_file_order,
step = step,
seed = seed,
shuffle_input = shuffle_input,
file_limit = file_limit,
path_file_log = path_file_log,
reverse_complement = reverse_complement,
reverse_complement_encoding = FALSE,
num_targets = 1,
ones_column = 1,
ambiguous_nuc = ambiguous_nuc,
proportion_per_seq = proportion_per_seq,
read_data = FALSE,
use_quality_score = use_quality_score,
padding = padding,
added_label_path = added_label_path,
add_input_as_seq = add_input_as_seq,
skip_amb_nuc = skip_amb_nuc,
max_samples = max_samples,
concat_seq = concat_seq,
file_filter = file_filter,
use_coverage = use_coverage,
proportion_entries = proportion_entries,
sample_by_file_size = sample_by_file_size,
n_gram = n_gram,
n_gram_stride = n_gram_stride,
masked_lm = NULL,
add_noise = add_noise,
return_int = return_int)
function() {
if (is.null(added_label_path)) {
xy <- gen()[[1]]
} else {
z <- gen()[[1]]
added_input <- z[1:(length(z)-1)]
xy <- z[length(z)][[1]]
}
xy_list <- slice_tensor_lm(xy = xy,
output_format = output_format,
target_len = target_len,
n_gram = n_gram,
# maxlen_n_gram = maxlen_n_gram,
# target_len_n_gram = target_len_n_gram,
n_gram_stride = n_gram_stride,
total_seq_len = total_seq_len,
return_int = return_int)
if (!is.null(added_label_path)) {
xy_list <- (list(append(added_input, list(xy_list$x)), xy_list$y))
}
if (reshape_xy_bool) {
xy_list <- f_reshape(x = xy_list$x, y = xy_list$y,
reshape_xy = reshape_xy,
reshape_x_bool = reshape_x_bool,
reshape_y_bool = reshape_y_bool,
reshape_sw_bool = FALSE, sw = NULL)
}
return(xy_list)
}
}
GenomeNet/deepG documentation built on Dec. 24, 2024, 12:11 p.m.
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Defines functions generator_fasta_lm
Documented in generator_fasta_lm
#' Language model generator for fasta/fastq files
#'
#' @description Iterates over folder containing fasta/fastq files and produces encoding of predictor sequences
#' and target variables. Will take a sequence of fixed size and use some part of sequence as input and other part as target.
#'
#' @inheritParams train_model
#' @param path_corpus Input directory where fasta files are located or path to single file ending with fasta or fastq
#' (as specified in format argument). Can also be a list of directories and/or files.
#' @param format File format, either `"fasta"` or `"fastq"`.
#' @param batch_size Number of samples in one batch.
#' @param maxlen Length of predictor sequence.
#' @param max_iter Stop after `max_iter` number of iterations failed to produce a new batch.
#' @param shuffle_file_order Logical, whether to go through files randomly or sequentially.
#' @param step How often to take a sample.
#' @param seed Sets seed for `set.seed` function for reproducible results.
#' @param shuffle_input Whether to shuffle entries in every fasta/fastq file before extracting samples.
#' @param verbose Whether to show messages.
#' @param path_file_log Write name of files to csv file if path is specified.
#' @param reverse_complement Boolean, for every new file decide randomly to use original data or its reverse complement.
#' @param ambiguous_nuc How to handle nucleotides outside vocabulary, either `"zero"`, `"discard"`, `"empirical"` or `"equal"`.
#' \itemize{
#' \item If `"zero"`, input gets encoded as zero vector.
#' \item If `"equal"`, input is repetition of `1/length(vocabulary)`.
#' \item If `"discard"`, samples containing nucleotides outside vocabulary get discarded.
#' \item If `"empirical"`, use nucleotide distribution of current file.
#' }
#' @param proportion_per_seq Numerical value between 0 and 1. Proportion of sequence to take samples from (use random subsequence).
#' @param use_quality_score Whether to use fastq quality scores. If 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).
#' @param padding Whether to pad sequences too short for one sample with zeros.
#' @param 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.
#' @param 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 `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 `TRUE`, 12234 gets one-hot encoded, so added input is a 3D tensor. If \code{add_input_as_seq} is
#' `FALSE` this will feed network just raw data (a 2D tensor).
#' @param skip_amb_nuc Threshold of ambiguous nucleotides to accept in fasta entry. Complete entry will get discarded otherwise.
#' @param max_samples Maximum number of samples to use from one file. If not `NULL` and file has more than \code{max_samples} samples, will randomly choose a
#' subset of \code{max_samples} samples.
#' @param concat_seq Character string or `NULL`. If not `NULL` all entries from file get concatenated to one sequence with `concat_seq` string between them.
#' Example: If 1.entry AACC, 2. entry TTTG and `concat_seq = "ZZZ"` this becomes AACCZZZTTTG.
#' @param target_len Number of nucleotides to predict at once for language model.
#' @param file_filter Vector of file names to use from path_corpus.
#' @param use_coverage Integer or `NULL`. If not `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 `"cov_n"` in the header, where `n` is some integer.
#' @param proportion_entries Proportion of fasta entries to keep. For example, if fasta file has 50 entries and `proportion_entries = 0.1`,
#' will randomly select 5 entries.
#' @param sample_by_file_size Sample new file weighted by file size (bigger files more likely).
#' @param n_gram Integer, encode target not nucleotide wise but combine n nucleotides at once. For example for `n=2, "AA" -> (1, 0,..., 0),`
#' `"AC" -> (0, 1, 0,..., 0), "TT" -> (0,..., 0, 1)`, where the one-hot vectors have length `length(vocabulary)^n`.
#' @param add_noise `NULL` or list of arguments. If not `NULL`, list must contain the following arguments: \code{noise_type} can be `"normal"` or `"uniform"`;
#' optional arguments `sd` or `mean` if noise_type is `"normal"` (default is `sd=1` and `mean=0`) or `min, max` if `noise_type` is `"uniform"`
#' (default is `min=0, max=1`).
#' @param return_int Whether to return integer encoding or one-hot encoding.
#' @param 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:
#' `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.
#' @rawNamespace import(data.table, except = c(first, last, between))
#' @importFrom magrittr %>%
#' @examplesIf reticulate::py_module_available("tensorflow")
#' # create dummy fasta files
#' path_input_1 <- tempfile()
#' dir.create(path_input_1)
#' create_dummy_data(file_path = path_input_1,
#' num_files = 2,
#' seq_length = 8,
#' num_seq = 1,
#' vocabulary = c("a", "c", "g", "t"))
#'
#' gen <- generator_fasta_lm(path_corpus = path_input_1, batch_size = 2,
#' maxlen = 7)
#' z <- gen()
#' dim(z[[1]])
#' z[[2]]
#'
#' @returns A generator function.
#' @export
generator_fasta_lm <- function(path_corpus,
format = "fasta",
batch_size = 256,
maxlen = 250,
max_iter = 10000,
vocabulary = c("a", "c", "g", "t"),
verbose = FALSE,
shuffle_file_order = FALSE,
step = 1,
seed = 1234,
shuffle_input = FALSE,
file_limit = NULL,
path_file_log = NULL,
reverse_complement = FALSE,
output_format = "target_right",
ambiguous_nuc = "zeros",
use_quality_score = FALSE,
proportion_per_seq = NULL,
padding = TRUE,
added_label_path = NULL,
add_input_as_seq = NULL,
skip_amb_nuc = NULL,
max_samples = NULL,
concat_seq = NULL,
target_len = 1,
file_filter = NULL,
use_coverage = NULL,
proportion_entries = NULL,
sample_by_file_size = FALSE,
n_gram = NULL,
n_gram_stride = 1,
add_noise = NULL,
return_int = FALSE,
reshape_xy = NULL) {
##TODO: add check for n-gram and option for stride
# if (!is.null(n_gram) & !(any(n_gram_stride == c(n_gram, 1)))) {
# stop("When using language model with n_gram encoding, n_gram_stride must be 1 or equal to n_gram")
# }
if (!is.null(n_gram)) {
# maxlen_n_gram <- ceiling((maxlen - n_gram + 1)/n_gram_stride)
# target_len_n_gram <- ceiling((target_len - n_gram + 1)/n_gram_stride)
if (!n_gram_stride == n_gram) {
stop("When using train_type='lm' with n_gram encoding, n_gram_stride must be equal to n_gram.")
}
} # else {
# maxlen_n_gram <- maxlen
# target_len_n_gram <- target_len
# }
if (!is.null(reshape_xy)) {
reshape_xy_bool <- TRUE
reshape_x_bool <- ifelse(is.null(reshape_xy$x), FALSE, TRUE)
if (reshape_x_bool && !all(c('x', 'y') %in% formals(reshape_xy$x))) {
stop("function reshape_xy$x needs to have arguments named x and y")
}
reshape_y_bool <- ifelse(is.null(reshape_xy$y), FALSE, TRUE)
if (reshape_y_bool && !all(c('x', 'y') %in% formals(reshape_xy$y))) {
stop("function reshape_xy$y needs to have arguments named x and y")
}
} else {
reshape_xy_bool <- FALSE
}
total_seq_len <- maxlen + target_len
gen <- generator_fasta_label_folder(path_corpus = path_corpus,
format = format,
batch_size = batch_size,
maxlen = total_seq_len,
max_iter = max_iter,
vocabulary = vocabulary,
shuffle_file_order = shuffle_file_order,
step = step,
seed = seed,
shuffle_input = shuffle_input,
file_limit = file_limit,
path_file_log = path_file_log,
reverse_complement = reverse_complement,
reverse_complement_encoding = FALSE,
num_targets = 1,
ones_column = 1,
ambiguous_nuc = ambiguous_nuc,
proportion_per_seq = proportion_per_seq,
read_data = FALSE,
use_quality_score = use_quality_score,
padding = padding,
added_label_path = added_label_path,
add_input_as_seq = add_input_as_seq,
skip_amb_nuc = skip_amb_nuc,
max_samples = max_samples,
concat_seq = concat_seq,
file_filter = file_filter,
use_coverage = use_coverage,
proportion_entries = proportion_entries,
sample_by_file_size = sample_by_file_size,
n_gram = n_gram,
n_gram_stride = n_gram_stride,
masked_lm = NULL,
add_noise = add_noise,
return_int = return_int)
function() {
if (is.null(added_label_path)) {
xy <- gen()[[1]]
} else {
z <- gen()[[1]]
added_input <- z[1:(length(z)-1)]
xy <- z[length(z)][[1]]
}
xy_list <- slice_tensor_lm(xy = xy,
output_format = output_format,
target_len = target_len,
n_gram = n_gram,
# maxlen_n_gram = maxlen_n_gram,
# target_len_n_gram = target_len_n_gram,
n_gram_stride = n_gram_stride,
total_seq_len = total_seq_len,
return_int = return_int)
if (!is.null(added_label_path)) {
xy_list <- (list(append(added_input, list(xy_list$x)), xy_list$y))
}
if (reshape_xy_bool) {
xy_list <- f_reshape(x = xy_list$x, y = xy_list$y,
reshape_xy = reshape_xy,
reshape_x_bool = reshape_x_bool,
reshape_y_bool = reshape_y_bool,
reshape_sw_bool = FALSE, sw = NULL)
}
return(xy_list)
}
}
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