#!/usr/bin/env bash
# Bulk download script for GSE126263
# Generated from Yeo Lab Publications Database
# Total files: 15

OUTDIR="GSE126263"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126263/suppl/GSE126263_MB002_Msi1_reproducible_peaks.bed.gz" -O "GSE126263_MB002_Msi1_reproducible_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126263/suppl/GSE126263_NSC201cb_Msi1_reproducible_peaks.bed.gz" -O "GSE126263_NSC201cb_Msi1_reproducible_peaks.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE126nnn/GSE126263/suppl/GSE126263_RAW.tar" -O "GSE126263_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 "SRR8548827"
gz1="$(_compress_if_exists 'SRR8548827_1' || true)"
gz2="$(_compress_if_exists 'SRR8548827_2' || true)"
gzs="$(_compress_if_exists 'SRR8548827' || true)"

fasterq-dump --split-files "SRR8548828"
gz1="$(_compress_if_exists 'SRR8548828_1' || true)"
gz2="$(_compress_if_exists 'SRR8548828_2' || true)"
gzs="$(_compress_if_exists 'SRR8548828' || true)"

fasterq-dump --split-files "SRR8548829"
gz1="$(_compress_if_exists 'SRR8548829_1' || true)"
gz2="$(_compress_if_exists 'SRR8548829_2' || true)"
gzs="$(_compress_if_exists 'SRR8548829' || true)"

fasterq-dump --split-files "SRR8548830"
gz1="$(_compress_if_exists 'SRR8548830_1' || true)"
gz2="$(_compress_if_exists 'SRR8548830_2' || true)"
gzs="$(_compress_if_exists 'SRR8548830' || true)"

fasterq-dump --split-files "SRR8548831"
gz1="$(_compress_if_exists 'SRR8548831_1' || true)"
gz2="$(_compress_if_exists 'SRR8548831_2' || true)"
gzs="$(_compress_if_exists 'SRR8548831' || true)"

fasterq-dump --split-files "SRR8548832"
gz1="$(_compress_if_exists 'SRR8548832_1' || true)"
gz2="$(_compress_if_exists 'SRR8548832_2' || true)"
gzs="$(_compress_if_exists 'SRR8548832' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548827/SRR8548827"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548828/SRR8548828"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548829/SRR8548829"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548830/SRR8548830"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548831/SRR8548831"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548832/SRR8548832"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548827/SRR8548827"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548828/SRR8548828"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548829/SRR8548829"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548830/SRR8548830"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548831/SRR8548831"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8548832/SRR8548832"

echo "Download complete. Files saved to $OUTDIR"