#!/usr/bin/env bash
# Bulk download script for GSE254208
# Generated from Yeo Lab Knowledgebase
# Total files: 12

OUTDIR=GSE254208
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE254nnn/GSE254208/suppl/GSE254208_down_regulated.csv.gz -O GSE254208_down_regulated.csv.gz
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE254nnn/GSE254208/suppl/GSE254208_down_regulated_sig.csv.gz -O GSE254208_down_regulated_sig.csv.gz
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE254nnn/GSE254208/suppl/GSE254208_up_regulated.csv.gz -O GSE254208_up_regulated.csv.gz
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE254nnn/GSE254208/suppl/GSE254208_up_regulated_sig.csv.gz -O GSE254208_up_regulated_sig.csv.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 SRR27726253
gz1="$(_compress_if_exists SRR27726253_1 || true)"
gz2="$(_compress_if_exists SRR27726253_2 || true)"
gzs="$(_compress_if_exists SRR27726253 || true)"

fasterq-dump --split-files SRR27726254
gz1="$(_compress_if_exists SRR27726254_1 || true)"
gz2="$(_compress_if_exists SRR27726254_2 || true)"
gzs="$(_compress_if_exists SRR27726254 || true)"

fasterq-dump --split-files SRR27726255
gz1="$(_compress_if_exists SRR27726255_1 || true)"
gz2="$(_compress_if_exists SRR27726255_2 || true)"
gzs="$(_compress_if_exists SRR27726255 || true)"

fasterq-dump --split-files SRR27726256
gz1="$(_compress_if_exists SRR27726256_1 || true)"
gz2="$(_compress_if_exists SRR27726256_2 || true)"
gzs="$(_compress_if_exists SRR27726256 || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726253/SRR27726253.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726254/SRR27726254.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726255/SRR27726255.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726256/SRR27726256.lite.1

# --- Additional data files ---
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726253/SRR27726253.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726254/SRR27726254.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726255/SRR27726255.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos13/sra-pub-zq-1305/SRR027/27726/SRR27726256/SRR27726256.lite.1

echo "Download complete. Files saved to $OUTDIR"