#!/usr/bin/env bash
# Bulk download script for GSE27218
# Generated from Yeo Lab Publications Database
# Total files: 43

OUTDIR="GSE27218"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27218/suppl/GSE27218_RAW.tar" -O "GSE27218_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 "SRR107061"
gz1="$(_compress_if_exists 'SRR107061_1' || true)"
gz2="$(_compress_if_exists 'SRR107061_2' || true)"
gzs="$(_compress_if_exists 'SRR107061' || true)"

fasterq-dump --split-files "SRR107062"
gz1="$(_compress_if_exists 'SRR107062_1' || true)"
gz2="$(_compress_if_exists 'SRR107062_2' || true)"
gzs="$(_compress_if_exists 'SRR107062' || true)"

fasterq-dump --split-files "SRR107063"
gz1="$(_compress_if_exists 'SRR107063_1' || true)"
gz2="$(_compress_if_exists 'SRR107063_2' || true)"
gzs="$(_compress_if_exists 'SRR107063' || true)"

fasterq-dump --split-files "SRR107064"
gz1="$(_compress_if_exists 'SRR107064_1' || true)"
gz2="$(_compress_if_exists 'SRR107064_2' || true)"
gzs="$(_compress_if_exists 'SRR107064' || true)"

fasterq-dump --split-files "SRR107065"
gz1="$(_compress_if_exists 'SRR107065_1' || true)"
gz2="$(_compress_if_exists 'SRR107065_2' || true)"
gzs="$(_compress_if_exists 'SRR107065' || true)"

fasterq-dump --split-files "SRR107066"
gz1="$(_compress_if_exists 'SRR107066_1' || true)"
gz2="$(_compress_if_exists 'SRR107066_2' || true)"
gzs="$(_compress_if_exists 'SRR107066' || true)"

fasterq-dump --split-files "SRR107067"
gz1="$(_compress_if_exists 'SRR107067_1' || true)"
gz2="$(_compress_if_exists 'SRR107067_2' || true)"
gzs="$(_compress_if_exists 'SRR107067' || true)"

fasterq-dump --split-files "SRR107068"
gz1="$(_compress_if_exists 'SRR107068_1' || true)"
gz2="$(_compress_if_exists 'SRR107068_2' || true)"
gzs="$(_compress_if_exists 'SRR107068' || true)"

fasterq-dump --split-files "SRR107069"
gz1="$(_compress_if_exists 'SRR107069_1' || true)"
gz2="$(_compress_if_exists 'SRR107069_2' || true)"
gzs="$(_compress_if_exists 'SRR107069' || true)"

fasterq-dump --split-files "SRR107070"
gz1="$(_compress_if_exists 'SRR107070_1' || true)"
gz2="$(_compress_if_exists 'SRR107070_2' || true)"
gzs="$(_compress_if_exists 'SRR107070' || true)"

fasterq-dump --split-files "SRR107071"
gz1="$(_compress_if_exists 'SRR107071_1' || true)"
gz2="$(_compress_if_exists 'SRR107071_2' || true)"
gzs="$(_compress_if_exists 'SRR107071' || true)"

fasterq-dump --split-files "SRR107072"
gz1="$(_compress_if_exists 'SRR107072_1' || true)"
gz2="$(_compress_if_exists 'SRR107072_2' || true)"
gzs="$(_compress_if_exists 'SRR107072' || true)"

fasterq-dump --split-files "SRR107073"
gz1="$(_compress_if_exists 'SRR107073_1' || true)"
gz2="$(_compress_if_exists 'SRR107073_2' || true)"
gzs="$(_compress_if_exists 'SRR107073' || true)"

fasterq-dump --split-files "SRR107074"
gz1="$(_compress_if_exists 'SRR107074_1' || true)"
gz2="$(_compress_if_exists 'SRR107074_2' || true)"
gzs="$(_compress_if_exists 'SRR107074' || true)"

fasterq-dump --split-files "SRR107075"
gz1="$(_compress_if_exists 'SRR107075_1' || true)"
gz2="$(_compress_if_exists 'SRR107075_2' || true)"
gzs="$(_compress_if_exists 'SRR107075' || true)"

fasterq-dump --split-files "SRR107076"
gz1="$(_compress_if_exists 'SRR107076_1' || true)"
gz2="$(_compress_if_exists 'SRR107076_2' || true)"
gzs="$(_compress_if_exists 'SRR107076' || true)"

fasterq-dump --split-files "SRR107077"
gz1="$(_compress_if_exists 'SRR107077_1' || true)"
gz2="$(_compress_if_exists 'SRR107077_2' || true)"
gzs="$(_compress_if_exists 'SRR107077' || true)"

fasterq-dump --split-files "SRR107078"
gz1="$(_compress_if_exists 'SRR107078_1' || true)"
gz2="$(_compress_if_exists 'SRR107078_2' || true)"
gzs="$(_compress_if_exists 'SRR107078' || true)"

fasterq-dump --split-files "SRR107079"
gz1="$(_compress_if_exists 'SRR107079_1' || true)"
gz2="$(_compress_if_exists 'SRR107079_2' || true)"
gzs="$(_compress_if_exists 'SRR107079' || true)"

fasterq-dump --split-files "SRR107080"
gz1="$(_compress_if_exists 'SRR107080_1' || true)"
gz2="$(_compress_if_exists 'SRR107080_2' || true)"
gzs="$(_compress_if_exists 'SRR107080' || true)"

fasterq-dump --split-files "SRR107081"
gz1="$(_compress_if_exists 'SRR107081_1' || true)"
gz2="$(_compress_if_exists 'SRR107081_2' || true)"
gzs="$(_compress_if_exists 'SRR107081' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107061/SRR107061"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107062/SRR107062"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107063/SRR107063"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107064/SRR107064"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107065/SRR107065"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107066/SRR107066"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107067/SRR107067"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107068/SRR107068"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107069/SRR107069"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107070/SRR107070"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107071/SRR107071"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107072/SRR107072"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107073/SRR107073"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107074/SRR107074"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107075/SRR107075"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107076/SRR107076"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107077/SRR107077"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107078/SRR107078"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107079/SRR107079"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107080/SRR107080"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107081/SRR107081"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107061/SRR107061"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107062/SRR107062"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107063/SRR107063"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107064/SRR107064"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107065/SRR107065"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107066/SRR107066"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107067/SRR107067"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107068/SRR107068"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107069/SRR107069"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107070/SRR107070"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107071/SRR107071"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107072/SRR107072"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107073/SRR107073"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107074/SRR107074"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107075/SRR107075"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107076/SRR107076"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107077/SRR107077"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107078/SRR107078"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107079/SRR107079"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107080/SRR107080"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR107081/SRR107081"

echo "Download complete. Files saved to $OUTDIR"