#!/usr/bin/env bash
# Bulk download script for GSE135435
# Generated from Yeo Lab Publications Database
# Total files: 17

OUTDIR="GSE135435"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE135nnn/GSE135435/suppl/GSE135435_RAW.tar" -O "GSE135435_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 "SRR9909221"
gz1="$(_compress_if_exists 'SRR9909221_1' || true)"
gz2="$(_compress_if_exists 'SRR9909221_2' || true)"
gzs="$(_compress_if_exists 'SRR9909221' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_1_Hera_S59_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_1_Hera_S59_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909222"
gz1="$(_compress_if_exists 'SRR9909222_1' || true)"
gz2="$(_compress_if_exists 'SRR9909222_2' || true)"
gzs="$(_compress_if_exists 'SRR9909222' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_2_Hera_S62_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_2_Hera_S62_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909223"
gz1="$(_compress_if_exists 'SRR9909223_1' || true)"
gz2="$(_compress_if_exists 'SRR9909223_2' || true)"
gzs="$(_compress_if_exists 'SRR9909223' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_3_Hera_S65_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_3_Hera_S65_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909224"
gz1="$(_compress_if_exists 'SRR9909224_1' || true)"
gz2="$(_compress_if_exists 'SRR9909224_2' || true)"
gzs="$(_compress_if_exists 'SRR9909224' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_4_Hera_S40_L003_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_4_Hera_S40_L003_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909225"
gz1="$(_compress_if_exists 'SRR9909225_1' || true)"
gz2="$(_compress_if_exists 'SRR9909225_2' || true)"
gzs="$(_compress_if_exists 'SRR9909225' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_1_Input_S57_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_1_Input_S57_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909226"
gz1="$(_compress_if_exists 'SRR9909226_1' || true)"
gz2="$(_compress_if_exists 'SRR9909226_2' || true)"
gzs="$(_compress_if_exists 'SRR9909226' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_2_Input_S60_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_2_Input_S60_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909227"
gz1="$(_compress_if_exists 'SRR9909227_1' || true)"
gz2="$(_compress_if_exists 'SRR9909227_2' || true)"
gzs="$(_compress_if_exists 'SRR9909227' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_3_Input_S63_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_3_Input_S63_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR9909228"
gz1="$(_compress_if_exists 'SRR9909228_1' || true)"
gz2="$(_compress_if_exists 'SRR9909228_2' || true)"
gzs="$(_compress_if_exists 'SRR9909228' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "DK_Hera_4_Input_S38_L003_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "DK_Hera_4_Input_S38_L003_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/SRR9909221/SRR9909221"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909222/SRR9909222"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909223/SRR9909223"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909224/SRR9909224"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909225/SRR9909225"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909226/SRR9909226"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909227/SRR9909227"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909228/SRR9909228"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909221/SRR9909221"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909225/SRR9909225"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909222/SRR9909222"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909226/SRR9909226"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909223/SRR9909223"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909227/SRR9909227"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909224/SRR9909224"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9909228/SRR9909228"

echo "Download complete. Files saved to $OUTDIR"