pull_char_uuids.R

In kimberlyroche/codaDE: What the Package Does in One 'Title Case' Line

source("path_fix.R")

library(RSQLite)
library(dplyr)
library(optparse)

option_list = list(
  make_option(c("--p"), type = "numeric", default = NULL,
              help = "number of features", metavar = "numeric")
);

opt_parser = OptionParser(option_list = option_list);
opt = parse_args(opt_parser);

p <- opt$p
file <- paste0("input_char_", p, ".txt")

conn <- dbConnect(RSQLite::SQLite(), file.path("output", "simulations.db"))

all_uuids <- dbGetQuery(conn, paste0("SELECT UUID FROM datasets WHERE P = ",p,";"))$UUID
wishlist <- data.frame(uuid = c(), baseline = c(), partial_info = c(), result_type = c())
counter <- 1
for(u in 1:length(all_uuids)) {
  if(u %% 100 == 0) {
    cat(paste0("UUID ", u, " / ", length(all_uuids), "\n"))
  }
  uuid <- all_uuids[u]
  for(type in c("relative_abundances", "scaled_ALDEx2", "scaled_DESeq2", "scaled_scran", "cpm")) {
    if(type == "relative_abundances") {
      for(par in c(0, 1)) {
        res <- dbGetQuery(conn, paste0("SELECT * FROM characteristics ",
                                       "WHERE UUID = '",uuid,"' AND ",
                                       "PARTIAL=", par, " AND TYPE='relative_abundances';"))
        # Look for any missing fields
        if(nrow(res) == 0 || any(is.na(res %>% select(-c(UUID, PARTIAL))))) {
          wishlist <- rbind(wishlist,
                            data.frame(ID = counter, uuid = uuid, partial_info = par, type = "relative_abundances"))
          counter <- counter + 1
        }
      }
    } else {
      res <- dbGetQuery(conn, paste0("SELECT * FROM characteristics ",
                                       "WHERE UUID = '",uuid,"' AND TYPE='",type,"';"))
      # Look for any missing fields
      if(nrow(res) == 0 || any(is.na(res %>% select(-c(UUID, PARTIAL, TYPE))))) {
        wishlist <- rbind(wishlist,
                          data.frame(ID = counter, uuid = uuid, partial_info = 0, type = type))
        counter <- counter + 1
      }
    }
  }
}

dbDisconnect(conn)

write.table(wishlist, file)