#!/usr/bin/env bash
# Bulk download script for GSE125954
# Generated from Yeo Lab Publications Database
# Total files: 28

OUTDIR="GSE125954"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125954/suppl/GSE125954_RAW.tar" -O "GSE125954_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 "SRR8511935"
gz1="$(_compress_if_exists 'SRR8511935_1' || true)"
gz2="$(_compress_if_exists 'SRR8511935_2' || true)"
gzs="$(_compress_if_exists 'SRR8511935' || true)"

fasterq-dump --split-files "SRR8511936"
gz1="$(_compress_if_exists 'SRR8511936_1' || true)"
gz2="$(_compress_if_exists 'SRR8511936_2' || true)"
gzs="$(_compress_if_exists 'SRR8511936' || true)"

fasterq-dump --split-files "SRR8511937"
gz1="$(_compress_if_exists 'SRR8511937_1' || true)"
gz2="$(_compress_if_exists 'SRR8511937_2' || true)"
gzs="$(_compress_if_exists 'SRR8511937' || true)"

fasterq-dump --split-files "SRR8511938"
gz1="$(_compress_if_exists 'SRR8511938_1' || true)"
gz2="$(_compress_if_exists 'SRR8511938_2' || true)"
gzs="$(_compress_if_exists 'SRR8511938' || true)"

fasterq-dump --split-files "SRR8511939"
gz1="$(_compress_if_exists 'SRR8511939_1' || true)"
gz2="$(_compress_if_exists 'SRR8511939_2' || true)"
gzs="$(_compress_if_exists 'SRR8511939' || true)"

fasterq-dump --split-files "SRR8511940"
gz1="$(_compress_if_exists 'SRR8511940_1' || true)"
gz2="$(_compress_if_exists 'SRR8511940_2' || true)"
gzs="$(_compress_if_exists 'SRR8511940' || true)"

fasterq-dump --split-files "SRR8511941"
gz1="$(_compress_if_exists 'SRR8511941_1' || true)"
gz2="$(_compress_if_exists 'SRR8511941_2' || true)"
gzs="$(_compress_if_exists 'SRR8511941' || true)"

fasterq-dump --split-files "SRR8511942"
gz1="$(_compress_if_exists 'SRR8511942_1' || true)"
gz2="$(_compress_if_exists 'SRR8511942_2' || true)"
gzs="$(_compress_if_exists 'SRR8511942' || true)"

fasterq-dump --split-files "SRR8511943"
gz1="$(_compress_if_exists 'SRR8511943_1' || true)"
gz2="$(_compress_if_exists 'SRR8511943_2' || true)"
gzs="$(_compress_if_exists 'SRR8511943' || true)"

fasterq-dump --split-files "SRR8511944"
gz1="$(_compress_if_exists 'SRR8511944_1' || true)"
gz2="$(_compress_if_exists 'SRR8511944_2' || true)"
gzs="$(_compress_if_exists 'SRR8511944' || true)"

fasterq-dump --split-files "SRR8511945"
gz1="$(_compress_if_exists 'SRR8511945_1' || true)"
gz2="$(_compress_if_exists 'SRR8511945_2' || true)"
gzs="$(_compress_if_exists 'SRR8511945' || true)"

fasterq-dump --split-files "SRR8511946"
gz1="$(_compress_if_exists 'SRR8511946_1' || true)"
gz2="$(_compress_if_exists 'SRR8511946_2' || true)"
gzs="$(_compress_if_exists 'SRR8511946' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511935/SRR8511935"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511936/SRR8511936"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511937/SRR8511937"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511938/SRR8511938"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511939/SRR8511939"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511940/SRR8511940"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511941/SRR8511941"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511942/SRR8511942"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511943/SRR8511943"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511944/SRR8511944"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511945/SRR8511945"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511946/SRR8511946"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511937/SRR8511937"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511938/SRR8511938"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511935/SRR8511935"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511936/SRR8511936"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511939/SRR8511939"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511940/SRR8511940"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511943/SRR8511943"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511944/SRR8511944"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511941/SRR8511941"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511942/SRR8511942"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511945/SRR8511945"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511946/SRR8511946"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511935/SRR8511935"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511938/SRR8511938"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8511940/SRR8511940"

echo "Download complete. Files saved to $OUTDIR"