#!/usr/bin/env bash
# Bulk download script for GSE167466
# Generated from Yeo Lab Publications Database
# Total files: 29

OUTDIR="GSE167466"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167466/suppl/GSE167466_1P_vs_1N.vs.2P_vs_2N.bed.gz" -O "GSE167466_1P_vs_1N.vs.2P_vs_2N.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167466/suppl/GSE167466_1P_vs_8P.vs.2P_vs_9P.bed.gz" -O "GSE167466_1P_vs_8P.vs.2P_vs_9P.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167466/suppl/GSE167466_4P_IP_vs_11P_input_IDR_6P_IP_vs_12P_input.bed.gz" -O "GSE167466_4P_IP_vs_11P_input_IDR_6P_IP_vs_12P_input.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167466/suppl/GSE167466_4P_IP_vs_4N_input_IDR_6P_IP_vs_6N_input.bed.gz" -O "GSE167466_4P_IP_vs_4N_input_IDR_6P_IP_vs_6N_input.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE167nnn/GSE167466/suppl/GSE167466_RAW.tar" -O "GSE167466_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 "SRR13779885"
gz1="$(_compress_if_exists 'SRR13779885_1' || true)"
gz2="$(_compress_if_exists 'SRR13779885_2' || true)"
gzs="$(_compress_if_exists 'SRR13779885' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "V5_CAS9_1N_S1_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779886"
gz1="$(_compress_if_exists 'SRR13779886_1' || true)"
gz2="$(_compress_if_exists 'SRR13779886_2' || true)"
gzs="$(_compress_if_exists 'SRR13779886' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "V5_CAS9_1P_S2_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779887"
gz1="$(_compress_if_exists 'SRR13779887_1' || true)"
gz2="$(_compress_if_exists 'SRR13779887_2' || true)"
gzs="$(_compress_if_exists 'SRR13779887' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Assa_2N_S60_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779888"
gz1="$(_compress_if_exists 'SRR13779888_1' || true)"
gz2="$(_compress_if_exists 'SRR13779888_2' || true)"
gzs="$(_compress_if_exists 'SRR13779888' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Assa_2P_S61_L005_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779889"
gz1="$(_compress_if_exists 'SRR13779889_1' || true)"
gz2="$(_compress_if_exists 'SRR13779889_2' || true)"
gzs="$(_compress_if_exists 'SRR13779889' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "V5_pCDNA_8P_S9_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779890"
gz1="$(_compress_if_exists 'SRR13779890_1' || true)"
gz2="$(_compress_if_exists 'SRR13779890_2' || true)"
gzs="$(_compress_if_exists 'SRR13779890' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "V5_pCDNA_9P_S10_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779891"
gz1="$(_compress_if_exists 'SRR13779891_1' || true)"
gz2="$(_compress_if_exists 'SRR13779891_2' || true)"
gzs="$(_compress_if_exists 'SRR13779891' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FLAG_CAS9_4N_S5_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779892"
gz1="$(_compress_if_exists 'SRR13779892_1' || true)"
gz2="$(_compress_if_exists 'SRR13779892_2' || true)"
gzs="$(_compress_if_exists 'SRR13779892' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FLAG_CAS9_4P_S6_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779893"
gz1="$(_compress_if_exists 'SRR13779893_1' || true)"
gz2="$(_compress_if_exists 'SRR13779893_2' || true)"
gzs="$(_compress_if_exists 'SRR13779893' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FLAG_CAS9_6N_S7_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779894"
gz1="$(_compress_if_exists 'SRR13779894_1' || true)"
gz2="$(_compress_if_exists 'SRR13779894_2' || true)"
gzs="$(_compress_if_exists 'SRR13779894' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FLAG_CAS9_6P_S8_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779895"
gz1="$(_compress_if_exists 'SRR13779895_1' || true)"
gz2="$(_compress_if_exists 'SRR13779895_2' || true)"
gzs="$(_compress_if_exists 'SRR13779895' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FLAG_pCDNA_11P_S11_L001_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR13779896"
gz1="$(_compress_if_exists 'SRR13779896_1' || true)"
gz2="$(_compress_if_exists 'SRR13779896_2' || true)"
gzs="$(_compress_if_exists 'SRR13779896' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "FLAG_pCDNA_12P_S12_L001_R1_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779885/SRR13779885"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779886/SRR13779886"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779887/SRR13779887"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779888/SRR13779888"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779889/SRR13779889"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779890/SRR13779890"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779891/SRR13779891"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779892/SRR13779892"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779893/SRR13779893"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779894/SRR13779894"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779895/SRR13779895"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779896/SRR13779896"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779887/SRR13779887"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779888/SRR13779888"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779891/SRR13779891"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779892/SRR13779892"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779893/SRR13779893"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779894/SRR13779894"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779895/SRR13779895"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779896/SRR13779896"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779885/SRR13779885"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779886/SRR13779886"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779889/SRR13779889"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR13779890/SRR13779890"

echo "Download complete. Files saved to $OUTDIR"