#!/usr/bin/env bash
# Bulk download script for GSE157917
# Generated from Yeo Lab Publications Database
# Total files: 53

OUTDIR="GSE157917"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE157nnn/GSE157917/suppl/GSE157917_RAW.tar" -O "GSE157917_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 "SRR12638141"
gz1="$(_compress_if_exists 'SRR12638141_1' || true)"
gz2="$(_compress_if_exists 'SRR12638141_2' || true)"
gzs="$(_compress_if_exists 'SRR12638141' || true)"

fasterq-dump --split-files "SRR12638142"
gz1="$(_compress_if_exists 'SRR12638142_1' || true)"
gz2="$(_compress_if_exists 'SRR12638142_2' || true)"
gzs="$(_compress_if_exists 'SRR12638142' || true)"

fasterq-dump --split-files "SRR12638143"
gz1="$(_compress_if_exists 'SRR12638143_1' || true)"
gz2="$(_compress_if_exists 'SRR12638143_2' || true)"
gzs="$(_compress_if_exists 'SRR12638143' || true)"

fasterq-dump --split-files "SRR12638144"
gz1="$(_compress_if_exists 'SRR12638144_1' || true)"
gz2="$(_compress_if_exists 'SRR12638144_2' || true)"
gzs="$(_compress_if_exists 'SRR12638144' || true)"

fasterq-dump --split-files "SRR12638145"
gz1="$(_compress_if_exists 'SRR12638145_1' || true)"
gz2="$(_compress_if_exists 'SRR12638145_2' || true)"
gzs="$(_compress_if_exists 'SRR12638145' || true)"

fasterq-dump --split-files "SRR12638146"
gz1="$(_compress_if_exists 'SRR12638146_1' || true)"
gz2="$(_compress_if_exists 'SRR12638146_2' || true)"
gzs="$(_compress_if_exists 'SRR12638146' || true)"

fasterq-dump --split-files "SRR12638147"
gz1="$(_compress_if_exists 'SRR12638147_1' || true)"
gz2="$(_compress_if_exists 'SRR12638147_2' || true)"
gzs="$(_compress_if_exists 'SRR12638147' || true)"

fasterq-dump --split-files "SRR12638148"
gz1="$(_compress_if_exists 'SRR12638148_1' || true)"
gz2="$(_compress_if_exists 'SRR12638148_2' || true)"
gzs="$(_compress_if_exists 'SRR12638148' || true)"

fasterq-dump --split-files "SRR12638149"
gz1="$(_compress_if_exists 'SRR12638149_1' || true)"
gz2="$(_compress_if_exists 'SRR12638149_2' || true)"
gzs="$(_compress_if_exists 'SRR12638149' || true)"

fasterq-dump --split-files "SRR12638150"
gz1="$(_compress_if_exists 'SRR12638150_1' || true)"
gz2="$(_compress_if_exists 'SRR12638150_2' || true)"
gzs="$(_compress_if_exists 'SRR12638150' || true)"

fasterq-dump --split-files "SRR12638151"
gz1="$(_compress_if_exists 'SRR12638151_1' || true)"
gz2="$(_compress_if_exists 'SRR12638151_2' || true)"
gzs="$(_compress_if_exists 'SRR12638151' || true)"

fasterq-dump --split-files "SRR12638152"
gz1="$(_compress_if_exists 'SRR12638152_1' || true)"
gz2="$(_compress_if_exists 'SRR12638152_2' || true)"
gzs="$(_compress_if_exists 'SRR12638152' || true)"

fasterq-dump --split-files "SRR12638153"
gz1="$(_compress_if_exists 'SRR12638153_1' || true)"
gz2="$(_compress_if_exists 'SRR12638153_2' || true)"
gzs="$(_compress_if_exists 'SRR12638153' || true)"

fasterq-dump --split-files "SRR12638154"
gz1="$(_compress_if_exists 'SRR12638154_1' || true)"
gz2="$(_compress_if_exists 'SRR12638154_2' || true)"
gzs="$(_compress_if_exists 'SRR12638154' || true)"

fasterq-dump --split-files "SRR12638155"
gz1="$(_compress_if_exists 'SRR12638155_1' || true)"
gz2="$(_compress_if_exists 'SRR12638155_2' || true)"
gzs="$(_compress_if_exists 'SRR12638155' || true)"

fasterq-dump --split-files "SRR12638156"
gz1="$(_compress_if_exists 'SRR12638156_1' || true)"
gz2="$(_compress_if_exists 'SRR12638156_2' || true)"
gzs="$(_compress_if_exists 'SRR12638156' || true)"

fasterq-dump --split-files "SRR12638157"
gz1="$(_compress_if_exists 'SRR12638157_1' || true)"
gz2="$(_compress_if_exists 'SRR12638157_2' || true)"
gzs="$(_compress_if_exists 'SRR12638157' || true)"

fasterq-dump --split-files "SRR12638158"
gz1="$(_compress_if_exists 'SRR12638158_1' || true)"
gz2="$(_compress_if_exists 'SRR12638158_2' || true)"
gzs="$(_compress_if_exists 'SRR12638158' || true)"

fasterq-dump --split-files "SRR12819255"
gz1="$(_compress_if_exists 'SRR12819255_1' || true)"
gz2="$(_compress_if_exists 'SRR12819255_2' || true)"
gzs="$(_compress_if_exists 'SRR12819255' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_HeLa_INPUT1_S5_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819256"
gz1="$(_compress_if_exists 'SRR12819256_1' || true)"
gz2="$(_compress_if_exists 'SRR12819256_2' || true)"
gzs="$(_compress_if_exists 'SRR12819256' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_HeLa_INPUT2_S7_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819257"
gz1="$(_compress_if_exists 'SRR12819257_1' || true)"
gz2="$(_compress_if_exists 'SRR12819257_2' || true)"
gzs="$(_compress_if_exists 'SRR12819257' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_K562_INPUT1_S1_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819258"
gz1="$(_compress_if_exists 'SRR12819258_1' || true)"
gz2="$(_compress_if_exists 'SRR12819258_2' || true)"
gzs="$(_compress_if_exists 'SRR12819258' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_K562_INPUT2_S3_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819259"
gz1="$(_compress_if_exists 'SRR12819259_1' || true)"
gz2="$(_compress_if_exists 'SRR12819259_2' || true)"
gzs="$(_compress_if_exists 'SRR12819259' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_HeLa_CLIP1_S6_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819260"
gz1="$(_compress_if_exists 'SRR12819260_1' || true)"
gz2="$(_compress_if_exists 'SRR12819260_2' || true)"
gzs="$(_compress_if_exists 'SRR12819260' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_HeLa_CLIP2_S8_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819261"
gz1="$(_compress_if_exists 'SRR12819261_1' || true)"
gz2="$(_compress_if_exists 'SRR12819261_2' || true)"
gzs="$(_compress_if_exists 'SRR12819261' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_K562_CLIP1_S2_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12819262"
gz1="$(_compress_if_exists 'SRR12819262_1' || true)"
gz2="$(_compress_if_exists 'SRR12819262_2' || true)"
gzs="$(_compress_if_exists 'SRR12819262' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "LUC7L2_K562_CLIP2_S4_L008_R1_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638141/SRR12638141"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638142/SRR12638142"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638143/SRR12638143"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638144/SRR12638144"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638145/SRR12638145"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638146/SRR12638146"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638147/SRR12638147"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638148/SRR12638148"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638149/SRR12638149"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638150/SRR12638150"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638151/SRR12638151"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638152/SRR12638152"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638153/SRR12638153"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638154/SRR12638154"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638155/SRR12638155"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638156/SRR12638156"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638157/SRR12638157"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638158/SRR12638158"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819255/SRR12819255"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819256/SRR12819256"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819257/SRR12819257"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819258/SRR12819258"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819259/SRR12819259"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819260/SRR12819260"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819261/SRR12819261"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819262/SRR12819262"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819259/SRR12819259"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819260/SRR12819260"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819255/SRR12819255"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819256/SRR12819256"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819261/SRR12819261"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819262/SRR12819262"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819257/SRR12819257"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12819258/SRR12819258"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638150/SRR12638150"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638151/SRR12638151"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638143/SRR12638143"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638153/SRR12638153"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638152/SRR12638152"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638154/SRR12638154"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638155/SRR12638155"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638156/SRR12638156"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638157/SRR12638157"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638158/SRR12638158"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638141/SRR12638141"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638142/SRR12638142"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638144/SRR12638144"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638145/SRR12638145"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638146/SRR12638146"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638147/SRR12638147"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638148/SRR12638148"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12638149/SRR12638149"

echo "Download complete. Files saved to $OUTDIR"