#!/usr/bin/env bash
# Bulk download script for GSE302600
# Generated from Yeo Lab Knowledgebase
# Total files: 13

OUTDIR=GSE302600
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE302nnn/GSE302600/suppl/GSE302600_ZFP697.reproducible_enriched_windows.tsv.gz -O GSE302600_ZFP697.reproducible_enriched_windows.tsv.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 SRR34550737
gz1="$(_compress_if_exists SRR34550737_1 || true)"
gz2="$(_compress_if_exists SRR34550737_2 || true)"
gzs="$(_compress_if_exists SRR34550737 || true)"

fasterq-dump --split-files SRR34550738
gz1="$(_compress_if_exists SRR34550738_1 || true)"
gz2="$(_compress_if_exists SRR34550738_2 || true)"
gzs="$(_compress_if_exists SRR34550738 || true)"

fasterq-dump --split-files SRR34550739
gz1="$(_compress_if_exists SRR34550739_1 || true)"
gz2="$(_compress_if_exists SRR34550739_2 || true)"
gzs="$(_compress_if_exists SRR34550739 || true)"

fasterq-dump --split-files SRR34550740
gz1="$(_compress_if_exists SRR34550740_1 || true)"
gz2="$(_compress_if_exists SRR34550740_2 || true)"
gzs="$(_compress_if_exists SRR34550740 || true)"

fasterq-dump --split-files SRR34550741
gz1="$(_compress_if_exists SRR34550741_1 || true)"
gz2="$(_compress_if_exists SRR34550741_2 || true)"
gzs="$(_compress_if_exists SRR34550741 || true)"

fasterq-dump --split-files SRR34550742
gz1="$(_compress_if_exists SRR34550742_1 || true)"
gz2="$(_compress_if_exists SRR34550742_2 || true)"
gzs="$(_compress_if_exists SRR34550742 || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550737/SRR34550737.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550738/SRR34550738.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550739/SRR34550739.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550740/SRR34550740.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550741/SRR34550741.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550742/SRR34550742.lite.1

# --- Additional data files ---
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550737/SRR34550737.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550738/SRR34550738.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550739/SRR34550739.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550740/SRR34550740.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550741/SRR34550741.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR034/34550/SRR34550742/SRR34550742.lite.1

echo "Download complete. Files saved to $OUTDIR"