inst/experiments/add_unigrams.R

In jakubkala/QuiPTsim:

library(parallel)
library(QuiPTsim)

add_unigrams <- function(old_dir, new_dir, RDSnames, alphabet, num.cores=35) {
  
  mclapply(RDSnames, function(n) {
    
    print(n)

    m <- readRDS(paste0(old_dir, n))
    m_with_uni <- cbind(count_ngrams(attr(m, "sequences"), alphabet = alphabet, 1), m)
    
    for (a in c("sequences", "motifs", "masks", "target")) {
      attr(m_with_uni, a) <- attr(m, a)
    }
    new_path <- paste0(new_dir, n)
    saveRDS(object = m_with_uni, file = new_path)
  }, mc.cores = num.cores)
}

old_dir <- "/home/jakubkala/projects/QuiPTsim-data/reduced_alph_enc_amylogram_encoding/"
new_dir <- "/home/jakubkala/projects/QuiPTsim-data/reduced_alph_enc_amylogram_encoding_unigram/"
paths <- dir(old_dir)

df <- read.csv(paste0(old_dir, paths[grepl("csv", paths)]))



RDSnames <- sapply(strsplit(x = df[["path"]], split = "/"), function(x) x[[3]])


add_unigrams(old_dir, new_dir, RDSnames, letters[1:6])