#!/usr/bin/env bash
# Bulk download script for GSE125808
# Generated from Yeo Lab Publications Database
# Total files: 74

OUTDIR="GSE125808"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125808/suppl/GSE125808_control_RPKM.csv.gz" -O "GSE125808_control_RPKM.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125808/suppl/GSE125808_sgRNA_RPKM.csv.gz" -O "GSE125808_sgRNA_RPKM.csv.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 "SRR8501380"
gz1="$(_compress_if_exists 'SRR8501380_1' || true)"
gz2="$(_compress_if_exists 'SRR8501380_2' || true)"
gzs="$(_compress_if_exists 'SRR8501380' || true)"

fasterq-dump --split-files "SRR8501381"
gz1="$(_compress_if_exists 'SRR8501381_1' || true)"
gz2="$(_compress_if_exists 'SRR8501381_2' || true)"
gzs="$(_compress_if_exists 'SRR8501381' || true)"

fasterq-dump --split-files "SRR8501382"
gz1="$(_compress_if_exists 'SRR8501382_1' || true)"
gz2="$(_compress_if_exists 'SRR8501382_2' || true)"
gzs="$(_compress_if_exists 'SRR8501382' || true)"

fasterq-dump --split-files "SRR8501383"
gz1="$(_compress_if_exists 'SRR8501383_1' || true)"
gz2="$(_compress_if_exists 'SRR8501383_2' || true)"
gzs="$(_compress_if_exists 'SRR8501383' || true)"

fasterq-dump --split-files "SRR8501384"
gz1="$(_compress_if_exists 'SRR8501384_1' || true)"
gz2="$(_compress_if_exists 'SRR8501384_2' || true)"
gzs="$(_compress_if_exists 'SRR8501384' || true)"

fasterq-dump --split-files "SRR8501385"
gz1="$(_compress_if_exists 'SRR8501385_1' || true)"
gz2="$(_compress_if_exists 'SRR8501385_2' || true)"
gzs="$(_compress_if_exists 'SRR8501385' || true)"

fasterq-dump --split-files "SRR8501386"
gz1="$(_compress_if_exists 'SRR8501386_1' || true)"
gz2="$(_compress_if_exists 'SRR8501386_2' || true)"
gzs="$(_compress_if_exists 'SRR8501386' || true)"

fasterq-dump --split-files "SRR8501387"
gz1="$(_compress_if_exists 'SRR8501387_1' || true)"
gz2="$(_compress_if_exists 'SRR8501387_2' || true)"
gzs="$(_compress_if_exists 'SRR8501387' || true)"

fasterq-dump --split-files "SRR8501388"
gz1="$(_compress_if_exists 'SRR8501388_1' || true)"
gz2="$(_compress_if_exists 'SRR8501388_2' || true)"
gzs="$(_compress_if_exists 'SRR8501388' || true)"

fasterq-dump --split-files "SRR8501389"
gz1="$(_compress_if_exists 'SRR8501389_1' || true)"
gz2="$(_compress_if_exists 'SRR8501389_2' || true)"
gzs="$(_compress_if_exists 'SRR8501389' || true)"

fasterq-dump --split-files "SRR8501390"
gz1="$(_compress_if_exists 'SRR8501390_1' || true)"
gz2="$(_compress_if_exists 'SRR8501390_2' || true)"
gzs="$(_compress_if_exists 'SRR8501390' || true)"

fasterq-dump --split-files "SRR8501391"
gz1="$(_compress_if_exists 'SRR8501391_1' || true)"
gz2="$(_compress_if_exists 'SRR8501391_2' || true)"
gzs="$(_compress_if_exists 'SRR8501391' || true)"

fasterq-dump --split-files "SRR8501392"
gz1="$(_compress_if_exists 'SRR8501392_1' || true)"
gz2="$(_compress_if_exists 'SRR8501392_2' || true)"
gzs="$(_compress_if_exists 'SRR8501392' || true)"

fasterq-dump --split-files "SRR8501393"
gz1="$(_compress_if_exists 'SRR8501393_1' || true)"
gz2="$(_compress_if_exists 'SRR8501393_2' || true)"
gzs="$(_compress_if_exists 'SRR8501393' || true)"

fasterq-dump --split-files "SRR8501394"
gz1="$(_compress_if_exists 'SRR8501394_1' || true)"
gz2="$(_compress_if_exists 'SRR8501394_2' || true)"
gzs="$(_compress_if_exists 'SRR8501394' || true)"

fasterq-dump --split-files "SRR8501395"
gz1="$(_compress_if_exists 'SRR8501395_1' || true)"
gz2="$(_compress_if_exists 'SRR8501395_2' || true)"
gzs="$(_compress_if_exists 'SRR8501395' || true)"

fasterq-dump --split-files "SRR8501396"
gz1="$(_compress_if_exists 'SRR8501396_1' || true)"
gz2="$(_compress_if_exists 'SRR8501396_2' || true)"
gzs="$(_compress_if_exists 'SRR8501396' || true)"

fasterq-dump --split-files "SRR8501397"
gz1="$(_compress_if_exists 'SRR8501397_1' || true)"
gz2="$(_compress_if_exists 'SRR8501397_2' || true)"
gzs="$(_compress_if_exists 'SRR8501397' || true)"

fasterq-dump --split-files "SRR8501398"
gz1="$(_compress_if_exists 'SRR8501398_1' || true)"
gz2="$(_compress_if_exists 'SRR8501398_2' || true)"
gzs="$(_compress_if_exists 'SRR8501398' || true)"

fasterq-dump --split-files "SRR8501399"
gz1="$(_compress_if_exists 'SRR8501399_1' || true)"
gz2="$(_compress_if_exists 'SRR8501399_2' || true)"
gzs="$(_compress_if_exists 'SRR8501399' || true)"

fasterq-dump --split-files "SRR8501400"
gz1="$(_compress_if_exists 'SRR8501400_1' || true)"
gz2="$(_compress_if_exists 'SRR8501400_2' || true)"
gzs="$(_compress_if_exists 'SRR8501400' || true)"

fasterq-dump --split-files "SRR8501401"
gz1="$(_compress_if_exists 'SRR8501401_1' || true)"
gz2="$(_compress_if_exists 'SRR8501401_2' || true)"
gzs="$(_compress_if_exists 'SRR8501401' || true)"

fasterq-dump --split-files "SRR8501402"
gz1="$(_compress_if_exists 'SRR8501402_1' || true)"
gz2="$(_compress_if_exists 'SRR8501402_2' || true)"
gzs="$(_compress_if_exists 'SRR8501402' || true)"

fasterq-dump --split-files "SRR8501403"
gz1="$(_compress_if_exists 'SRR8501403_1' || true)"
gz2="$(_compress_if_exists 'SRR8501403_2' || true)"
gzs="$(_compress_if_exists 'SRR8501403' || true)"

fasterq-dump --split-files "SRR8501404"
gz1="$(_compress_if_exists 'SRR8501404_1' || true)"
gz2="$(_compress_if_exists 'SRR8501404_2' || true)"
gzs="$(_compress_if_exists 'SRR8501404' || true)"

fasterq-dump --split-files "SRR8501405"
gz1="$(_compress_if_exists 'SRR8501405_1' || true)"
gz2="$(_compress_if_exists 'SRR8501405_2' || true)"
gzs="$(_compress_if_exists 'SRR8501405' || true)"

fasterq-dump --split-files "SRR8501406"
gz1="$(_compress_if_exists 'SRR8501406_1' || true)"
gz2="$(_compress_if_exists 'SRR8501406_2' || true)"
gzs="$(_compress_if_exists 'SRR8501406' || true)"

fasterq-dump --split-files "SRR8501407"
gz1="$(_compress_if_exists 'SRR8501407_1' || true)"
gz2="$(_compress_if_exists 'SRR8501407_2' || true)"
gzs="$(_compress_if_exists 'SRR8501407' || true)"

fasterq-dump --split-files "SRR8501408"
gz1="$(_compress_if_exists 'SRR8501408_1' || true)"
gz2="$(_compress_if_exists 'SRR8501408_2' || true)"
gzs="$(_compress_if_exists 'SRR8501408' || true)"

fasterq-dump --split-files "SRR8501409"
gz1="$(_compress_if_exists 'SRR8501409_1' || true)"
gz2="$(_compress_if_exists 'SRR8501409_2' || true)"
gzs="$(_compress_if_exists 'SRR8501409' || true)"

fasterq-dump --split-files "SRR8501410"
gz1="$(_compress_if_exists 'SRR8501410_1' || true)"
gz2="$(_compress_if_exists 'SRR8501410_2' || true)"
gzs="$(_compress_if_exists 'SRR8501410' || true)"

fasterq-dump --split-files "SRR8501411"
gz1="$(_compress_if_exists 'SRR8501411_1' || true)"
gz2="$(_compress_if_exists 'SRR8501411_2' || true)"
gzs="$(_compress_if_exists 'SRR8501411' || true)"

fasterq-dump --split-files "SRR8501412"
gz1="$(_compress_if_exists 'SRR8501412_1' || true)"
gz2="$(_compress_if_exists 'SRR8501412_2' || true)"
gzs="$(_compress_if_exists 'SRR8501412' || true)"

fasterq-dump --split-files "SRR8501413"
gz1="$(_compress_if_exists 'SRR8501413_1' || true)"
gz2="$(_compress_if_exists 'SRR8501413_2' || true)"
gzs="$(_compress_if_exists 'SRR8501413' || true)"

fasterq-dump --split-files "SRR8501414"
gz1="$(_compress_if_exists 'SRR8501414_1' || true)"
gz2="$(_compress_if_exists 'SRR8501414_2' || true)"
gzs="$(_compress_if_exists 'SRR8501414' || true)"

fasterq-dump --split-files "SRR8501415"
gz1="$(_compress_if_exists 'SRR8501415_1' || true)"
gz2="$(_compress_if_exists 'SRR8501415_2' || true)"
gzs="$(_compress_if_exists 'SRR8501415' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501380/SRR8501380"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501381/SRR8501381"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501382/SRR8501382"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501383/SRR8501383"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501384/SRR8501384"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501385/SRR8501385"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501386/SRR8501386"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501387/SRR8501387"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501388/SRR8501388"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501389/SRR8501389"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501390/SRR8501390"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501391/SRR8501391"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501392/SRR8501392"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501393/SRR8501393"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501394/SRR8501394"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501395/SRR8501395"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501396/SRR8501396"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501397/SRR8501397"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501398/SRR8501398"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501399/SRR8501399"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501400/SRR8501400"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501401/SRR8501401"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501402/SRR8501402"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501403/SRR8501403"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501404/SRR8501404"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501405/SRR8501405"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501406/SRR8501406"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501407/SRR8501407"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501408/SRR8501408"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501409/SRR8501409"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501410/SRR8501410"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501411/SRR8501411"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501412/SRR8501412"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501413/SRR8501413"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501414/SRR8501414"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501415/SRR8501415"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501380/SRR8501380"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501381/SRR8501381"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501382/SRR8501382"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501383/SRR8501383"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501384/SRR8501384"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501385/SRR8501385"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501386/SRR8501386"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501387/SRR8501387"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501388/SRR8501388"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501389/SRR8501389"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501390/SRR8501390"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501391/SRR8501391"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501392/SRR8501392"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501393/SRR8501393"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501394/SRR8501394"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501395/SRR8501395"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501396/SRR8501396"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501397/SRR8501397"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501398/SRR8501398"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501399/SRR8501399"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501400/SRR8501400"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501401/SRR8501401"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501402/SRR8501402"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501403/SRR8501403"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501404/SRR8501404"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501405/SRR8501405"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501406/SRR8501406"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501407/SRR8501407"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501408/SRR8501408"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501409/SRR8501409"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501410/SRR8501410"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501411/SRR8501411"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501412/SRR8501412"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501413/SRR8501413"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501414/SRR8501414"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8501415/SRR8501415"

echo "Download complete. Files saved to $OUTDIR"