#!/usr/bin/env bash
# Bulk download script for GSE125125
# Generated from Yeo Lab Publications Database
# Total files: 42

OUTDIR="GSE125125"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125125/suppl/GSE125125_base_nontg_FUS_wt_het_gene.tsv.gz" -O "GSE125125_base_nontg_FUS_wt_het_gene.tsv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125125/suppl/GSE125125_base_nontg_FUS_wt_homo_gene.tsv.gz" -O "GSE125125_base_nontg_FUS_wt_homo_gene.tsv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125125/suppl/GSE125125_bs_control_fus_ko_wt_gene.tsv.gz" -O "GSE125125_bs_control_fus_ko_wt_gene.tsv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE125nnn/GSE125125/suppl/GSE125125_expression.tsv.gz" -O "GSE125125_expression.tsv.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 "SRR8444929"
gz1="$(_compress_if_exists 'SRR8444929_1' || true)"
gz2="$(_compress_if_exists 'SRR8444929_2' || true)"
gzs="$(_compress_if_exists 'SRR8444929' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_157.fastq.gz"
fi

fasterq-dump --split-files "SRR8444930"
gz1="$(_compress_if_exists 'SRR8444930_1' || true)"
gz2="$(_compress_if_exists 'SRR8444930_2' || true)"
gzs="$(_compress_if_exists 'SRR8444930' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_163.fastq.gz"
fi

fasterq-dump --split-files "SRR8444931"
gz1="$(_compress_if_exists 'SRR8444931_1' || true)"
gz2="$(_compress_if_exists 'SRR8444931_2' || true)"
gzs="$(_compress_if_exists 'SRR8444931' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_821.fastq.gz"
fi

fasterq-dump --split-files "SRR8444932"
gz1="$(_compress_if_exists 'SRR8444932_1' || true)"
gz2="$(_compress_if_exists 'SRR8444932_2' || true)"
gzs="$(_compress_if_exists 'SRR8444932' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "SC_540.fastq.gz"
fi

fasterq-dump --split-files "SRR8444933"
gz1="$(_compress_if_exists 'SRR8444933_1' || true)"
gz2="$(_compress_if_exists 'SRR8444933_2' || true)"
gzs="$(_compress_if_exists 'SRR8444933' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_545.fastq.gz"
fi

fasterq-dump --split-files "SRR8444934"
gz1="$(_compress_if_exists 'SRR8444934_1' || true)"
gz2="$(_compress_if_exists 'SRR8444934_2' || true)"
gzs="$(_compress_if_exists 'SRR8444934' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_825.fastq.gz"
fi

fasterq-dump --split-files "SRR8444935"
gz1="$(_compress_if_exists 'SRR8444935_1' || true)"
gz2="$(_compress_if_exists 'SRR8444935_2' || true)"
gzs="$(_compress_if_exists 'SRR8444935' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_166.fastq.gz"
fi

fasterq-dump --split-files "SRR8444936"
gz1="$(_compress_if_exists 'SRR8444936_1' || true)"
gz2="$(_compress_if_exists 'SRR8444936_2' || true)"
gzs="$(_compress_if_exists 'SRR8444936' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_858.fastq.gz"
fi

fasterq-dump --split-files "SRR8444937"
gz1="$(_compress_if_exists 'SRR8444937_1' || true)"
gz2="$(_compress_if_exists 'SRR8444937_2' || true)"
gzs="$(_compress_if_exists 'SRR8444937' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Sc_882.fastq.gz"
fi

fasterq-dump --split-files "SRR8444938"
gz1="$(_compress_if_exists 'SRR8444938_1' || true)"
gz2="$(_compress_if_exists 'SRR8444938_2' || true)"
gzs="$(_compress_if_exists 'SRR8444938' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "KQ_23_ATCACG_L006_R1.fastq.gz"
fi

fasterq-dump --split-files "SRR8444939"
gz1="$(_compress_if_exists 'SRR8444939_1' || true)"
gz2="$(_compress_if_exists 'SRR8444939_2' || true)"
gzs="$(_compress_if_exists 'SRR8444939' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "KQ_24_TTAGGC_L006_R1.fastq.gz"
fi

fasterq-dump --split-files "SRR8444940"
gz1="$(_compress_if_exists 'SRR8444940_1' || true)"
gz2="$(_compress_if_exists 'SRR8444940_2' || true)"
gzs="$(_compress_if_exists 'SRR8444940' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "KQ_25_ACTTGA_L006_R1.fastq.gz"
fi

fasterq-dump --split-files "SRR8444941"
gz1="$(_compress_if_exists 'SRR8444941_1' || true)"
gz2="$(_compress_if_exists 'SRR8444941_2' || true)"
gzs="$(_compress_if_exists 'SRR8444941' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "KQ_27_TAGCTT_L006_R1.fastq.gz"
fi

fasterq-dump --split-files "SRR8444942"
gz1="$(_compress_if_exists 'SRR8444942_1' || true)"
gz2="$(_compress_if_exists 'SRR8444942_2' || true)"
gzs="$(_compress_if_exists 'SRR8444942' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "KQ_28_GGCTAC_L006_R1.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444929/SRR8444929"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444930/SRR8444930"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444931/SRR8444931"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444932/SRR8444932"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444933/SRR8444933"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444934/SRR8444934"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444935/SRR8444935"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444936/SRR8444936"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444937/SRR8444937"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444938/SRR8444938"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444939/SRR8444939"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444940/SRR8444940"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444941/SRR8444941"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444942/SRR8444942"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444938/SRR8444938"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444939/SRR8444939"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444940/SRR8444940"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444941/SRR8444941"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444942/SRR8444942"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444929/SRR8444929"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444930/SRR8444930"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444935/SRR8444935"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444932/SRR8444932"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444933/SRR8444933"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444931/SRR8444931"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444934/SRR8444934"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444936/SRR8444936"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444937/SRR8444937"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444929/SRR8444929"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444930/SRR8444930"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444931/SRR8444931"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444932/SRR8444932"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444933/SRR8444933"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444935/SRR8444935"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444936/SRR8444936"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444938/SRR8444938"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR008/444/SRR8444939/SRR8444939.sralite.1"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8444941/SRR8444941"

echo "Download complete. Files saved to $OUTDIR"