#!/usr/bin/env bash
# Bulk download script for GSE328331
# Generated from Yeo Lab Knowledgebase
# Total files: 16

OUTDIR=GSE328331
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- 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 SRR38147810
gz1="$(_compress_if_exists SRR38147810_1 || true)"
gz2="$(_compress_if_exists SRR38147810_2 || true)"
gzs="$(_compress_if_exists SRR38147810 || true)"

fasterq-dump --split-files SRR38147811
gz1="$(_compress_if_exists SRR38147811_1 || true)"
gz2="$(_compress_if_exists SRR38147811_2 || true)"
gzs="$(_compress_if_exists SRR38147811 || true)"

fasterq-dump --split-files SRR38147812
gz1="$(_compress_if_exists SRR38147812_1 || true)"
gz2="$(_compress_if_exists SRR38147812_2 || true)"
gzs="$(_compress_if_exists SRR38147812 || true)"

fasterq-dump --split-files SRR38147813
gz1="$(_compress_if_exists SRR38147813_1 || true)"
gz2="$(_compress_if_exists SRR38147813_2 || true)"
gzs="$(_compress_if_exists SRR38147813 || true)"

fasterq-dump --split-files SRR38147814
gz1="$(_compress_if_exists SRR38147814_1 || true)"
gz2="$(_compress_if_exists SRR38147814_2 || true)"
gzs="$(_compress_if_exists SRR38147814 || true)"

fasterq-dump --split-files SRR38147815
gz1="$(_compress_if_exists SRR38147815_1 || true)"
gz2="$(_compress_if_exists SRR38147815_2 || true)"
gzs="$(_compress_if_exists SRR38147815 || true)"

fasterq-dump --split-files SRR38147816
gz1="$(_compress_if_exists SRR38147816_1 || true)"
gz2="$(_compress_if_exists SRR38147816_2 || true)"
gzs="$(_compress_if_exists SRR38147816 || true)"

fasterq-dump --split-files SRR38147817
gz1="$(_compress_if_exists SRR38147817_1 || true)"
gz2="$(_compress_if_exists SRR38147817_2 || true)"
gzs="$(_compress_if_exists SRR38147817 || 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/SRR038/38147/SRR38147810/SRR38147810.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147811/SRR38147811.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147812/SRR38147812.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147813/SRR38147813.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147814/SRR38147814.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147815/SRR38147815.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147816/SRR38147816.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147817/SRR38147817.sralite.1

# --- Additional data files ---
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147810/SRR38147810.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147811/SRR38147811.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147812/SRR38147812.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147813/SRR38147813.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147814/SRR38147814.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147815/SRR38147815.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147816/SRR38147816.sralite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR038/38147/SRR38147817/SRR38147817.sralite.1

echo "Download complete. Files saved to $OUTDIR"