#!/usr/bin/env bash
# Bulk download script for GSE213469
# Generated from Yeo Lab Publications Database
# Total files: 17

OUTDIR="GSE213469"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE213nnn/GSE213469/suppl/GSE213469_filtered_peak_bc_matrix.h5" -O "GSE213469_filtered_peak_bc_matrix.h5"

# --- 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 "SRR21594569"
gz1="$(_compress_if_exists 'SRR21594569_1' || true)"
gz2="$(_compress_if_exists 'SRR21594569_2' || true)"
gzs="$(_compress_if_exists 'SRR21594569' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Cl13_Spl_1_S21_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Cl13_Spl_1_S21_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594570"
gz1="$(_compress_if_exists 'SRR21594570_1' || true)"
gz2="$(_compress_if_exists 'SRR21594570_2' || true)"
gzs="$(_compress_if_exists 'SRR21594570' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Cl13_Spl_2_S22_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Cl13_Spl_2_S22_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594571"
gz1="$(_compress_if_exists 'SRR21594571_1' || true)"
gz2="$(_compress_if_exists 'SRR21594571_2' || true)"
gzs="$(_compress_if_exists 'SRR21594571' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Cl13_Spl_3_S23_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Cl13_Spl_3_S23_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594572"
gz1="$(_compress_if_exists 'SRR21594572_1' || true)"
gz2="$(_compress_if_exists 'SRR21594572_2' || true)"
gzs="$(_compress_if_exists 'SRR21594572' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Cl13_Spl_4_S24_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Cl13_Spl_4_S24_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594573"
gz1="$(_compress_if_exists 'SRR21594573_1' || true)"
gz2="$(_compress_if_exists 'SRR21594573_2' || true)"
gzs="$(_compress_if_exists 'SRR21594573' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Arm_Spl_1_S17_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Arm_Spl_1_S17_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594574"
gz1="$(_compress_if_exists 'SRR21594574_1' || true)"
gz2="$(_compress_if_exists 'SRR21594574_2' || true)"
gzs="$(_compress_if_exists 'SRR21594574' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Arm_Spl_2_S18_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Arm_Spl_2_S18_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594575"
gz1="$(_compress_if_exists 'SRR21594575_1' || true)"
gz2="$(_compress_if_exists 'SRR21594575_2' || true)"
gzs="$(_compress_if_exists 'SRR21594575' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Arm_Spl_3_S19_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Arm_Spl_3_S19_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR21594576"
gz1="$(_compress_if_exists 'SRR21594576_1' || true)"
gz2="$(_compress_if_exists 'SRR21594576_2' || true)"
gzs="$(_compress_if_exists 'SRR21594576' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Div1_Arm_Spl_4_S20_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Div1_Arm_Spl_4_S20_L001_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/SRR21594569/SRR21594569"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594570/SRR21594570"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594571/SRR21594571"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594572/SRR21594572"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594573/SRR21594573"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594574/SRR21594574"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594575/SRR21594575"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594576/SRR21594576"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594573/SRR21594573"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594574/SRR21594574"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594575/SRR21594575"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594576/SRR21594576"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594569/SRR21594569"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594570/SRR21594570"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594571/SRR21594571"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21594572/SRR21594572"

echo "Download complete. Files saved to $OUTDIR"