#!/usr/bin/env bash
# Bulk download script for GSE215252
# Generated from Yeo Lab Publications Database
# Total files: 7

OUTDIR="GSE215252"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE215nnn/GSE215252/suppl/GSE215252_RAW.tar" -O "GSE215252_RAW.tar"

# --- 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 "SRR21863810"
gz1="$(_compress_if_exists 'SRR21863810_1' || true)"
gz2="$(_compress_if_exists 'SRR21863810_2' || true)"
gzs="$(_compress_if_exists 'SRR21863810' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.out.sorted.bam.gz"
fi

fasterq-dump --split-files "SRR21863811"
gz1="$(_compress_if_exists 'SRR21863811_1' || true)"
gz2="$(_compress_if_exists 'SRR21863811_2' || true)"
gzs="$(_compress_if_exists 'SRR21863811' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.out.sorted.bam.gz"
fi

fasterq-dump --split-files "SRR21863812"
gz1="$(_compress_if_exists 'SRR21863812_1' || true)"
gz2="$(_compress_if_exists 'SRR21863812_2' || true)"
gzs="$(_compress_if_exists 'SRR21863812' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.out.sorted.bam.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21863810/SRR21863810"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21863811/SRR21863811"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21863812/SRR21863812"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21863812/SRR21863812"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21863811/SRR21863811"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21863810/SRR21863810"

echo "Download complete. Files saved to $OUTDIR"