#!/usr/bin/env bash
# Bulk download script for GSE290755
# Generated from Yeo Lab Knowledgebase
# Total files: 18

OUTDIR=GSE290755
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 SRR32538805
gz1="$(_compress_if_exists SRR32538805_1 || true)"
gz2="$(_compress_if_exists SRR32538805_2 || true)"
gzs="$(_compress_if_exists SRR32538805 || true)"

fasterq-dump --split-files SRR32538806
gz1="$(_compress_if_exists SRR32538806_1 || true)"
gz2="$(_compress_if_exists SRR32538806_2 || true)"
gzs="$(_compress_if_exists SRR32538806 || true)"

fasterq-dump --split-files SRR32538807
gz1="$(_compress_if_exists SRR32538807_1 || true)"
gz2="$(_compress_if_exists SRR32538807_2 || true)"
gzs="$(_compress_if_exists SRR32538807 || true)"

fasterq-dump --split-files SRR32538808
gz1="$(_compress_if_exists SRR32538808_1 || true)"
gz2="$(_compress_if_exists SRR32538808_2 || true)"
gzs="$(_compress_if_exists SRR32538808 || true)"

fasterq-dump --split-files SRR32538809
gz1="$(_compress_if_exists SRR32538809_1 || true)"
gz2="$(_compress_if_exists SRR32538809_2 || true)"
gzs="$(_compress_if_exists SRR32538809 || true)"

fasterq-dump --split-files SRR32538810
gz1="$(_compress_if_exists SRR32538810_1 || true)"
gz2="$(_compress_if_exists SRR32538810_2 || true)"
gzs="$(_compress_if_exists SRR32538810 || true)"

fasterq-dump --split-files SRR32538811
gz1="$(_compress_if_exists SRR32538811_1 || true)"
gz2="$(_compress_if_exists SRR32538811_2 || true)"
gzs="$(_compress_if_exists SRR32538811 || true)"

fasterq-dump --split-files SRR32538812
gz1="$(_compress_if_exists SRR32538812_1 || true)"
gz2="$(_compress_if_exists SRR32538812_2 || true)"
gzs="$(_compress_if_exists SRR32538812 || true)"

fasterq-dump --split-files SRR32538813
gz1="$(_compress_if_exists SRR32538813_1 || true)"
gz2="$(_compress_if_exists SRR32538813_2 || true)"
gzs="$(_compress_if_exists SRR32538813 || 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/SRR032/32538/SRR32538805/SRR32538805.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538806/SRR32538806.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538807/SRR32538807.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538808/SRR32538808.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538809/SRR32538809.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538810/SRR32538810.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538811/SRR32538811.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538812/SRR32538812.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538813/SRR32538813.lite.1

# --- Additional data files ---
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538805/SRR32538805.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538806/SRR32538806.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538807/SRR32538807.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538808/SRR32538808.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538809/SRR32538809.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538810/SRR32538810.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538811/SRR32538811.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538812/SRR32538812.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos10/sra-pub-zq-1002/SRR032/32538/SRR32538813/SRR32538813.lite.1

echo "Download complete. Files saved to $OUTDIR"