#!/usr/bin/env bash
# Bulk download script for GSE46240
# Generated from Yeo Lab Publications Database
# Total files: 30

OUTDIR="GSE46240"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46240/suppl/GSE46240_ChIP-seq_peaks_p53_binding_sites.txt.gz" -O "GSE46240_ChIP-seq_peaks_p53_binding_sites.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE46nnn/GSE46240/suppl/GSE46240_RAW.tar" -O "GSE46240_RAW.tar"

# --- SRA run files ---
# Tip: use 'fasterq-dump' from SRA Toolkit for FASTQ conversion
#      with optional renaming to original submitted FASTQ names.
# Set to 1 to rename SRR outputs (e.g. SRR_1.fastq.gz -> sample_R1.fastq.gz)
RENAME_SRA_TO_ORIGINAL=1

_compress_if_exists() {
  local stem="$1"
  if [ -f "${stem}.fastq" ]; then
    gzip -f "${stem}.fastq"
    echo "${stem}.fastq.gz"
    return 0
  fi
  if [ -f "${stem}.fq" ]; then
    gzip -f "${stem}.fq"
    echo "${stem}.fq.gz"
    return 0
  fi
  return 1
}

# Option A: Download via SRA Toolkit (recommended)
fasterq-dump --split-files "SRR832846"
gz1="$(_compress_if_exists 'SRR832846_1' || true)"
gz2="$(_compress_if_exists 'SRR832846_2' || true)"
gzs="$(_compress_if_exists 'SRR832846' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "p53_ChIP-seq_wt_MEF.fastq.gz"
fi

fasterq-dump --split-files "SRR832847"
gz1="$(_compress_if_exists 'SRR832847_1' || true)"
gz2="$(_compress_if_exists 'SRR832847_2' || true)"
gzs="$(_compress_if_exists 'SRR832847' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "input_wt_MEF.fastq.gz"
fi

fasterq-dump --split-files "SRR832848"
gz1="$(_compress_if_exists 'SRR832848_1' || true)"
gz2="$(_compress_if_exists 'SRR832848_2' || true)"
gzs="$(_compress_if_exists 'SRR832848' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "p53_ChIP-seq_p53KO_MEF.fastq.gz"
fi

fasterq-dump --split-files "SRR832849"
gz1="$(_compress_if_exists 'SRR832849_1' || true)"
gz2="$(_compress_if_exists 'SRR832849_2' || true)"
gzs="$(_compress_if_exists 'SRR832849' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "input_p53KO_MEF.fastq.gz"
fi

fasterq-dump --split-files "SRR832850"
gz1="$(_compress_if_exists 'SRR832850_1' || true)"
gz2="$(_compress_if_exists 'SRR832850_2' || true)"
gzs="$(_compress_if_exists 'SRR832850' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "wt_MEF_ ut_replicate-1.fastq.gz"
fi

fasterq-dump --split-files "SRR832851"
gz1="$(_compress_if_exists 'SRR832851_1' || true)"
gz2="$(_compress_if_exists 'SRR832851_2' || true)"
gzs="$(_compress_if_exists 'SRR832851' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "wt_MEF_ dox_replicate-1.fastq.gz"
fi

fasterq-dump --split-files "SRR832852"
gz1="$(_compress_if_exists 'SRR832852_1' || true)"
gz2="$(_compress_if_exists 'SRR832852_2' || true)"
gzs="$(_compress_if_exists 'SRR832852' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "wt_MEF_ ut_replicate-2.fastq.gz"
fi

fasterq-dump --split-files "SRR832853"
gz1="$(_compress_if_exists 'SRR832853_1' || true)"
gz2="$(_compress_if_exists 'SRR832853_2' || true)"
gzs="$(_compress_if_exists 'SRR832853' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "wt_MEF_ dox_replicate-2.fastq.gz"
fi

fasterq-dump --split-files "SRR832854"
gz1="$(_compress_if_exists 'SRR832854_1' || true)"
gz2="$(_compress_if_exists 'SRR832854_2' || true)"
gzs="$(_compress_if_exists 'SRR832854' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "wt_MEF_ ut_replicate-3.fastq.gz"
fi

fasterq-dump --split-files "SRR832855"
gz1="$(_compress_if_exists 'SRR832855_1' || true)"
gz2="$(_compress_if_exists 'SRR832855_2' || true)"
gzs="$(_compress_if_exists 'SRR832855' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "wt_MEF_ dox_replicate-3.fastq.gz"
fi

fasterq-dump --split-files "SRR832856"
gz1="$(_compress_if_exists 'SRR832856_1' || true)"
gz2="$(_compress_if_exists 'SRR832856_2' || true)"
gzs="$(_compress_if_exists 'SRR832856' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "p53KO_MEF_ ut_replicate-1.fastq.gz"
fi

fasterq-dump --split-files "SRR832857"
gz1="$(_compress_if_exists 'SRR832857_1' || true)"
gz2="$(_compress_if_exists 'SRR832857_2' || true)"
gzs="$(_compress_if_exists 'SRR832857' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "p53KO_MEF_ dox_replicate-1.fastq.gz"
fi

fasterq-dump --split-files "SRR832858"
gz1="$(_compress_if_exists 'SRR832858_1' || true)"
gz2="$(_compress_if_exists 'SRR832858_2' || true)"
gzs="$(_compress_if_exists 'SRR832858' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "p53KO_MEF_ ut_replicate-2.fastq.gz"
fi

fasterq-dump --split-files "SRR832859"
gz1="$(_compress_if_exists 'SRR832859_1' || true)"
gz2="$(_compress_if_exists 'SRR832859_2' || true)"
gzs="$(_compress_if_exists 'SRR832859' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "p53KO_MEF_ dox_replicate-2.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832846/SRR832846.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832847/SRR832847.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832848/SRR832848.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832849/SRR832849.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832850/SRR832850.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832851/SRR832851.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832852/SRR832852.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832853/SRR832853.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832854/SRR832854.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832855/SRR832855.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832856/SRR832856.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832857/SRR832857.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832858/SRR832858.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832859/SRR832859.2"

# --- Additional data files ---
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832847/SRR832847.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832848/SRR832848.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832846/SRR832846.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832849/SRR832849.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832857/SRR832857.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832859/SRR832859.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832856/SRR832856.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832858/SRR832858.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832851/SRR832851.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832853/SRR832853.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832855/SRR832855.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832850/SRR832850.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832852/SRR832852.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/832/SRR832854/SRR832854.2"

echo "Download complete. Files saved to $OUTDIR"