#!/usr/bin/env bash
# Bulk download script for GSE243675
# Generated from Yeo Lab Publications Database
# Total files: 19

OUTDIR="GSE243675"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE243nnn/GSE243675/suppl/GSE243675_RAW.tar" -O "GSE243675_RAW.tar"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE243nnn/GSE243675/suppl/GSE243675_SA_gp61-sfGFP_rep1.vs.SA_gp61-sfGFP_rep2.bed.gz" -O "GSE243675_SA_gp61-sfGFP_rep1.vs.SA_gp61-sfGFP_rep2.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE243nnn/GSE243675/suppl/GSE243675_SA_sfGFP_rep1.vs.SA_sfGFP_rep2.bed.gz" -O "GSE243675_SA_sfGFP_rep1.vs.SA_sfGFP_rep2.bed.gz"

# --- 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 "SRR26130299"
gz1="$(_compress_if_exists 'SRR26130299_1' || true)"
gz2="$(_compress_if_exists 'SRR26130299_2' || true)"
gzs="$(_compress_if_exists 'SRR26130299' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_gp61-sfGFP_IN_2_S5_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_gp61-sfGFP_IN_2_S5_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130300"
gz1="$(_compress_if_exists 'SRR26130300_1' || true)"
gz2="$(_compress_if_exists 'SRR26130300_2' || true)"
gzs="$(_compress_if_exists 'SRR26130300' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_gp61-sfGFP_IN_1_S7_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_gp61-sfGFP_IN_1_S7_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130301"
gz1="$(_compress_if_exists 'SRR26130301_1' || true)"
gz2="$(_compress_if_exists 'SRR26130301_2' || true)"
gzs="$(_compress_if_exists 'SRR26130301' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_gp61-sfGFP_IP_2_S9_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_gp61-sfGFP_IP_2_S9_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130302"
gz1="$(_compress_if_exists 'SRR26130302_1' || true)"
gz2="$(_compress_if_exists 'SRR26130302_2' || true)"
gzs="$(_compress_if_exists 'SRR26130302' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_gp61-sfGFP_IP_1_S11_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_gp61-sfGFP_IP_1_S11_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130303"
gz1="$(_compress_if_exists 'SRR26130303_1' || true)"
gz2="$(_compress_if_exists 'SRR26130303_2' || true)"
gzs="$(_compress_if_exists 'SRR26130303' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_sfGFP_IN_2_S6_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_sfGFP_IN_2_S6_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130304"
gz1="$(_compress_if_exists 'SRR26130304_1' || true)"
gz2="$(_compress_if_exists 'SRR26130304_2' || true)"
gzs="$(_compress_if_exists 'SRR26130304' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_sfGFP_IN_1_S4_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_sfGFP_IN_1_S4_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130305"
gz1="$(_compress_if_exists 'SRR26130305_1' || true)"
gz2="$(_compress_if_exists 'SRR26130305_2' || true)"
gzs="$(_compress_if_exists 'SRR26130305' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_sfGFP_IP_2_S10_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_sfGFP_IP_2_S10_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR26130306"
gz1="$(_compress_if_exists 'SRR26130306_1' || true)"
gz2="$(_compress_if_exists 'SRR26130306_2' || true)"
gzs="$(_compress_if_exists 'SRR26130306' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_sfGFP_IP_1_S8_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_sfGFP_IP_1_S8_L002_R2_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130299/SRR26130299"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130300/SRR26130300"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130301/SRR26130301"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130302/SRR26130302"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130303/SRR26130303"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130304/SRR26130304"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130305/SRR26130305"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130306/SRR26130306"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130302/SRR26130302"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130301/SRR26130301"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130306/SRR26130306"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130305/SRR26130305"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130300/SRR26130300"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130299/SRR26130299"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130304/SRR26130304"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR26130303/SRR26130303"

echo "Download complete. Files saved to $OUTDIR"