#!/usr/bin/env bash
# Bulk download script for GSE240325
# Generated from Yeo Lab Publications Database
# Total files: 6

OUTDIR="GSE240325"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240325/suppl/GSE240325_RAW.tar" -O "GSE240325_RAW.tar"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE240nnn/GSE240325/suppl/GSE240325_apo_rbfox_insitu_clustered.sorted.filtered_lite.gff.gz" -O "GSE240325_apo_rbfox_insitu_clustered.sorted.filtered_lite.gff.gz"

# --- 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 "SRR25567593"
gz1="$(_compress_if_exists 'SRR25567593_1' || true)"
gz2="$(_compress_if_exists 'SRR25567593_2' || true)"
gzs="$(_compress_if_exists 'SRR25567593' || true)"

fasterq-dump --split-files "SRR25567594"
gz1="$(_compress_if_exists 'SRR25567594_1' || true)"
gz2="$(_compress_if_exists 'SRR25567594_2' || true)"
gzs="$(_compress_if_exists 'SRR25567594' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR025/25567/SRR25567593/SRR25567593.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR025/25567/SRR25567594/SRR25567594.1"

# --- Additional data files ---
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR025/25567/SRR25567594/SRR25567594.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-run-30/SRR025/25567/SRR25567593/SRR25567593.1"

echo "Download complete. Files saved to $OUTDIR"