#!/usr/bin/env bash
# Bulk download script for GSE175885
# Generated from Yeo Lab Publications Database
# Total files: 17

OUTDIR="GSE175885"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE175nnn/GSE175885/suppl/GSE175885_RAW.tar" -O "GSE175885_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 "SRR14699656"
gz1="$(_compress_if_exists 'SRR14699656_1' || true)"
gz2="$(_compress_if_exists 'SRR14699656_2' || true)"
gzs="$(_compress_if_exists 'SRR14699656' || true)"

fasterq-dump --split-files "SRR14699657"
gz1="$(_compress_if_exists 'SRR14699657_1' || true)"
gz2="$(_compress_if_exists 'SRR14699657_2' || true)"
gzs="$(_compress_if_exists 'SRR14699657' || true)"

fasterq-dump --split-files "SRR14699658"
gz1="$(_compress_if_exists 'SRR14699658_1' || true)"
gz2="$(_compress_if_exists 'SRR14699658_2' || true)"
gzs="$(_compress_if_exists 'SRR14699658' || true)"

fasterq-dump --split-files "SRR14699659"
gz1="$(_compress_if_exists 'SRR14699659_1' || true)"
gz2="$(_compress_if_exists 'SRR14699659_2' || true)"
gzs="$(_compress_if_exists 'SRR14699659' || true)"

fasterq-dump --split-files "SRR14699660"
gz1="$(_compress_if_exists 'SRR14699660_1' || true)"
gz2="$(_compress_if_exists 'SRR14699660_2' || true)"
gzs="$(_compress_if_exists 'SRR14699660' || true)"

fasterq-dump --split-files "SRR14699661"
gz1="$(_compress_if_exists 'SRR14699661_1' || true)"
gz2="$(_compress_if_exists 'SRR14699661_2' || true)"
gzs="$(_compress_if_exists 'SRR14699661' || true)"

fasterq-dump --split-files "SRR14699662"
gz1="$(_compress_if_exists 'SRR14699662_1' || true)"
gz2="$(_compress_if_exists 'SRR14699662_2' || true)"
gzs="$(_compress_if_exists 'SRR14699662' || true)"

fasterq-dump --split-files "SRR14699663"
gz1="$(_compress_if_exists 'SRR14699663_1' || true)"
gz2="$(_compress_if_exists 'SRR14699663_2' || true)"
gzs="$(_compress_if_exists 'SRR14699663' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699656/SRR14699656"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699657/SRR14699657"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699658/SRR14699658"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699659/SRR14699659"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699660/SRR14699660"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699661/SRR14699661"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699662/SRR14699662"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699663/SRR14699663"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699662/SRR14699662"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699663/SRR14699663"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699658/SRR14699658"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699659/SRR14699659"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699660/SRR14699660"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699661/SRR14699661"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699656/SRR14699656"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14699657/SRR14699657"

echo "Download complete. Files saved to $OUTDIR"