---
title: "14-Apul-RepeatMasker"
author: "Kathleen Durkin"
date: "2024-11-08"
always_allow_html: true
output: 
  bookdown::html_document2:
    theme: cosmo
    toc: true
    toc_float: true
    number_sections: true
    code_folding: show
    code_download: true
  github_document:
    toc: true
    toc_depth: 3
    number_sections: true
    html_preview: true 
---

```{r setup, include=FALSE}
library(knitr)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = TRUE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```

One of the probable ways sncRNAs influence gene expression and interact with DNA methylation is through suppression of transposable elements. RepeatMasker will ID repeated elements in the genome likely to be TEs. 

We'll be using the (currently unpublished) A.pulchra genome assembled by collaborators, Apulchra-genome.fa, which was also used for sncRNA discovery in `11-Apul-sRNA-ShortStack_4.1.0-pulchra_genome`

This is a modified version of [Sam White's existing Mox script](https://robertslab.github.io/sams-notebook/posts/2023/2023-05-26-Repeats-Identification---P.meandrina-Using-RepeatMasker-on-Mox/index.html) for running RepeatMasker.

```{r, engine='bash'}

## Assign Variables

# Set number of CPUs to use
threads=28

# Species to use for RepeatMasker
species="cnidaria"

# Paths to programs
repeatmasker="/home/shared/RepeatMasker-4.1.7-p1/RepeatMasker"

# Input files/directories
genome_index_dir="../data/"
genome_fasta="${genome_index_dir}/Apulchra-genome.fa"

# Programs associative array
declare -A programs_array
programs_array=(
[repeatmasker]="${repeatmasker}"
)

###################################################################################################

# Exit script if any command fails
set -e

# Load Python Mox module for Python3 module availability
#module load intel-python3_2017

# SegFault fix?
export THREADS_DAEMON_MODEL=1

# #### Run RepeatMasker with _all_ species setting and following options:
# 
# -species "all" : Sets species to all
# 
# -par ${cpus} : Use n CPU threads
# 
# -gff : Create GFF output file (in addition to default files)
# 
# -excln : Adjusts output table calculations to exclude sequence runs of >=25 Ns. Useful for draft genome assemblies.

"${programs_array[repeatmasker]}" \
${genome_fasta} \
-species ${species} \
-par ${threads} \
-gff \
-excln \
-dir .

# Generate checksums
echo ""
echo "Generating checksum for input FastA"
echo "${genome_fasta}..."

md5sum "${genome_fasta}" | tee --append checksums.md5

echo ""

for file in *
do
  echo ""
  echo "Generating checksum for ${file}..."
  echo ""

  md5sum "${file}" | tee --append checksums.md5

  echo ""
  echo "Checksum generated."
done


#######################################################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx/repeatmasker menu
    elif [[ "${program}" == "blastx" ]] \
    || [[ "${program}" == "repeatmasker" ]]; then
      ${programs_array[$program]} -help
    fi
    ${programs_array[$program]} -h
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
  echo "Finished logging programs options."
  echo ""
fi


# Document programs in PATH (primarily for program version ID)
echo "Logging system PATH..."

{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log

echo "Finished logging system $PATH."
echo ""

echo "Script complete!"

```