#!/usr/bin/env bash
# Bulk download script for GSE184564
# Generated from Yeo Lab Publications Database
# Total files: 16

OUTDIR="GSE184564"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_KO_metrics_summary.csv.gz" -O "GSE184564_KO_metrics_summary.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WT_metrics_summary.csv.gz" -O "GSE184564_WT_metrics_summary.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTonly_Lgr5+_Atoh1+_Sox4+_Dclk1+.csv.gz" -O "GSE184564_WTonly_Lgr5+_Atoh1+_Sox4+_Dclk1+.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTvsKO_Atoh1+.csv.gz" -O "GSE184564_WTvsKO_Atoh1+.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTvsKO_Chga.csv.gz" -O "GSE184564_WTvsKO_Chga.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTvsKO_DCLK1+.csv.gz" -O "GSE184564_WTvsKO_DCLK1+.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTvsKO_Klf4+.csv.gz" -O "GSE184564_WTvsKO_Klf4+.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTvsKO_Lyz1+.csv.gz" -O "GSE184564_WTvsKO_Lyz1+.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_WTvsKO_Sox4+.csv.gz" -O "GSE184564_WTvsKO_Sox4+.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_barcodes.tsv.gz" -O "GSE184564_barcodes.tsv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_features.tsv.gz" -O "GSE184564_features.tsv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE184nnn/GSE184564/suppl/GSE184564_matrix.mtx.gz" -O "GSE184564_matrix.mtx.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 "SRR15999537"
gz1="$(_compress_if_exists 'SRR15999537_1' || true)"
gz2="$(_compress_if_exists 'SRR15999537_2' || true)"
gzs="$(_compress_if_exists 'SRR15999537' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TL_WT_S8_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TL_WT_S8_L002_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR15999538"
gz1="$(_compress_if_exists 'SRR15999538_1' || true)"
gz2="$(_compress_if_exists 'SRR15999538_2' || true)"
gzs="$(_compress_if_exists 'SRR15999538' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "TL_KO_S9_L002_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "TL_KO_S9_L002_R2_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15999537/SRR15999537"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15999538/SRR15999538"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15999538/SRR15999538"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15999537/SRR15999537"

echo "Download complete. Files saved to $OUTDIR"