deleterious

Simulations of populations with deleterious mutations

We created a framework to simulate haplodiploid populations in the SLiM simulation framework. Here, we run simulations of populations with recessive deleterious mutations under a range of selective coefficients. The scripts used are the slim_scripts directory, and the results of the simulation run in the results directory.

Parse simulation results

We parsed the simulation results:

mkdir -p results/outputs
# manually move SLiM outputs to there

module load R parallel ruby

ls results/outputs \
  | cut -f 2 -d "/" \
  | ruby -pe 'gsub(/-output/, "")' \
  | parallel "grep -A50000 -m1 -e 'Generation, FixedMutations, NucleotideHeterozygosity' \
  results/outputs/{}-output/* | grep -v 'Generation' \
  | grep -v '^--'| cut -f 4- -d '/' > results/{}_tmp"

parse_df <- function(path) {
  df <- read.table(file.path("results",path))
  id <- as.character(df$V1)
  split_id <- strsplit(id, split = "_")

  ploidy    <- sapply(split_id, function(x) x[1])
  dominance <-  sapply(split_id, function(x) x[2])

  id <- sapply(split_id, function(x) x[3])
  split_id <- strsplit(id, split = "\\.")

  selection <- sapply(split_id, function(x) x[1])

  simulation_id <- sapply(split_id, function(x) paste(x[2], gsub("-.*", "", x[3]), sep = "_"))
  generation    <- sapply(split_id, function(x) gsub(".*-", "", x[3]))

  to_return <- data.frame(
    ploidy = ploidy,
    dominance = dominance,
    selection = selection,
    simulation_id = simulation_id,
    generation = generation,
    number_fixed = df$V2,
    nucleotide_diversity = df$V3
  )

  return(to_return)

}

to_parse <- list.files("results")
to_parse <- to_parse[grepl("_tmp", to_parse)]

parsed_df <- lapply(to_parse, function(path) parse_df(path))
parsed_df <- do.call(rbind, parsed_df)

parsed_df$selection <- as.character(parsed_df$selection)
parsed_df$selection <- gsub("s-", "-0.", parsed_df$selection)

write.csv(parsed_df,
          file="results/deleterious_mutations_h0.csv",
          row.names=FALSE, quote=FALSE)