#!/usr/bin/env bash
# Bulk download script for GSE104501
# Generated from Yeo Lab Publications Database
# Total files: 5

OUTDIR="GSE104501"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE104nnn/GSE104501/suppl/GSE104501_N2_TailLength.csv.gz" -O "GSE104501_N2_TailLength.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 "SRR6125154"
gz1="$(_compress_if_exists 'SRR6125154_1' || true)"
gz2="$(_compress_if_exists 'SRR6125154_2' || true)"
gzs="$(_compress_if_exists 'SRR6125154' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "rep1_3prime.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "rep1_5prime.fastq.gz"
fi

fasterq-dump --split-files "SRR6125155"
gz1="$(_compress_if_exists 'SRR6125155_1' || true)"
gz2="$(_compress_if_exists 'SRR6125155_2' || true)"
gzs="$(_compress_if_exists 'SRR6125155' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "rep2_3prime.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "rep2_5prime.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6125154/SRR6125154"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6125155/SRR6125155"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6125154/SRR6125154"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6125155/SRR6125155"

echo "Download complete. Files saved to $OUTDIR"