#!/usr/bin/env bash
# Bulk download script for GSE39872
# Generated from Yeo Lab Publications Database
# Total files: 19

OUTDIR="GSE39872"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39872/suppl/GSE39872_RAW.tar" -O "GSE39872_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 "SRR531463"
gz1="$(_compress_if_exists 'SRR531463_1' || true)"
gz2="$(_compress_if_exists 'SRR531463_2' || true)"
gzs="$(_compress_if_exists 'SRR531463' || true)"

fasterq-dump --split-files "SRR531464"
gz1="$(_compress_if_exists 'SRR531464_1' || true)"
gz2="$(_compress_if_exists 'SRR531464_2' || true)"
gzs="$(_compress_if_exists 'SRR531464' || true)"

fasterq-dump --split-files "SRR531465"
gz1="$(_compress_if_exists 'SRR531465_1' || true)"
gz2="$(_compress_if_exists 'SRR531465_2' || true)"
gzs="$(_compress_if_exists 'SRR531465' || true)"

fasterq-dump --split-files "SRR531466"
gz1="$(_compress_if_exists 'SRR531466_1' || true)"
gz2="$(_compress_if_exists 'SRR531466_2' || true)"
gzs="$(_compress_if_exists 'SRR531466' || true)"

fasterq-dump --split-files "SRR531467"
gz1="$(_compress_if_exists 'SRR531467_1' || true)"
gz2="$(_compress_if_exists 'SRR531467_2' || true)"
gzs="$(_compress_if_exists 'SRR531467' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "LIN28KD_H9_rnaseq.fastq.gz"
fi

fasterq-dump --split-files "SRR531468"
gz1="$(_compress_if_exists 'SRR531468_1' || true)"
gz2="$(_compress_if_exists 'SRR531468_2' || true)"
gzs="$(_compress_if_exists 'SRR531468' || true)"

fasterq-dump --split-files "SRR531469"
gz1="$(_compress_if_exists 'SRR531469_1' || true)"
gz2="$(_compress_if_exists 'SRR531469_2' || true)"
gzs="$(_compress_if_exists 'SRR531469' || true)"

fasterq-dump --split-files "SRR531470"
gz1="$(_compress_if_exists 'SRR531470_1' || true)"
gz2="$(_compress_if_exists 'SRR531470_2' || true)"
gzs="$(_compress_if_exists 'SRR531470' || true)"

fasterq-dump --split-files "SRR531471"
gz1="$(_compress_if_exists 'SRR531471_1' || true)"
gz2="$(_compress_if_exists 'SRR531471_2' || true)"
gzs="$(_compress_if_exists 'SRR531471' || true)"


# 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/SRR000/531/SRR531463/SRR531463.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531464/SRR531464.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531465/SRR531465.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531466/SRR531466.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531467/SRR531467.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531468/SRR531468.2"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR531469/SRR531469"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531470/SRR531470.2"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR531471/SRR531471"

# --- Additional data files ---
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531467/SRR531467.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531463/SRR531463.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531464/SRR531464.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531465/SRR531465.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531466/SRR531466.2"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531468/SRR531468.2"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR531469/SRR531469"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-run-32/SRR000/531/SRR531470/SRR531470.2"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR531471/SRR531471"

echo "Download complete. Files saved to $OUTDIR"