#!/usr/bin/env bash
# Bulk download script for GSE118347
# Generated from Yeo Lab Publications Database
# Total files: 30

OUTDIR="GSE118347"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118347/suppl/GSE118347_Tctransitions_endogenousFUS.tsv.gz" -O "GSE118347_Tctransitions_endogenousFUS.tsv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE118nnn/GSE118347/suppl/GSE118347_Tctransitions_flagFUS.tsv.gz" -O "GSE118347_Tctransitions_flagFUS.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 "SRR7664123"
gz1="$(_compress_if_exists 'SRR7664123_1' || true)"
gz2="$(_compress_if_exists 'SRR7664123_2' || true)"
gzs="$(_compress_if_exists 'SRR7664123' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_Flag_FUSwt_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664124"
gz1="$(_compress_if_exists 'SRR7664124_1' || true)"
gz2="$(_compress_if_exists 'SRR7664124_2' || true)"
gzs="$(_compress_if_exists 'SRR7664124' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_Flag_FUSwt_PAR_II.fastq.gz"
fi

fasterq-dump --split-files "SRR7664125"
gz1="$(_compress_if_exists 'SRR7664125_1' || true)"
gz2="$(_compress_if_exists 'SRR7664125_2' || true)"
gzs="$(_compress_if_exists 'SRR7664125' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Reseq_MNs_Flag_FUSwt_PAR_II.fastq.gz"
fi

fasterq-dump --split-files "SRR7664126"
gz1="$(_compress_if_exists 'SRR7664126_1' || true)"
gz2="$(_compress_if_exists 'SRR7664126_2' || true)"
gzs="$(_compress_if_exists 'SRR7664126' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_Flag_FUS525_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664127"
gz1="$(_compress_if_exists 'SRR7664127_1' || true)"
gz2="$(_compress_if_exists 'SRR7664127_2' || true)"
gzs="$(_compress_if_exists 'SRR7664127' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Reseq_MNs_Flag_FUS525_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664128"
gz1="$(_compress_if_exists 'SRR7664128_1' || true)"
gz2="$(_compress_if_exists 'SRR7664128_2' || true)"
gzs="$(_compress_if_exists 'SRR7664128' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_Flag_FUS525_PAR_II.fastq.gz"
fi

fasterq-dump --split-files "SRR7664129"
gz1="$(_compress_if_exists 'SRR7664129_1' || true)"
gz2="$(_compress_if_exists 'SRR7664129_2' || true)"
gzs="$(_compress_if_exists 'SRR7664129' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Reseq_MNs_Flag_FUS525_PAR_II.fastq.gz"
fi

fasterq-dump --split-files "SRR7664130"
gz1="$(_compress_if_exists 'SRR7664130_1' || true)"
gz2="$(_compress_if_exists 'SRR7664130_2' || true)"
gzs="$(_compress_if_exists 'SRR7664130' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_FUSwt_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664131"
gz1="$(_compress_if_exists 'SRR7664131_1' || true)"
gz2="$(_compress_if_exists 'SRR7664131_2' || true)"
gzs="$(_compress_if_exists 'SRR7664131' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Reseq_MNs_FUSwt_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664132"
gz1="$(_compress_if_exists 'SRR7664132_1' || true)"
gz2="$(_compress_if_exists 'SRR7664132_2' || true)"
gzs="$(_compress_if_exists 'SRR7664132' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_FUSwt_PAR_II.fastq.gz"
fi

fasterq-dump --split-files "SRR7664133"
gz1="$(_compress_if_exists 'SRR7664133_1' || true)"
gz2="$(_compress_if_exists 'SRR7664133_2' || true)"
gzs="$(_compress_if_exists 'SRR7664133' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_FUShm_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664134"
gz1="$(_compress_if_exists 'SRR7664134_1' || true)"
gz2="$(_compress_if_exists 'SRR7664134_2' || true)"
gzs="$(_compress_if_exists 'SRR7664134' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Reseq_MNs_FUShm_PAR_I.fastq.gz"
fi

fasterq-dump --split-files "SRR7664135"
gz1="$(_compress_if_exists 'SRR7664135_1' || true)"
gz2="$(_compress_if_exists 'SRR7664135_2' || true)"
gzs="$(_compress_if_exists 'SRR7664135' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "MNs_FUShm_PAR_II.fastq.gz"
fi

fasterq-dump --split-files "SRR7664136"
gz1="$(_compress_if_exists 'SRR7664136_1' || true)"
gz2="$(_compress_if_exists 'SRR7664136_2' || true)"
gzs="$(_compress_if_exists 'SRR7664136' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Reseq_MNs_FUShm_PAR_II.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664123/SRR7664123"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664124/SRR7664124"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664125/SRR7664125"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664126/SRR7664126"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664127/SRR7664127"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664128/SRR7664128"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664129/SRR7664129"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664130/SRR7664130"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664131/SRR7664131"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664132/SRR7664132"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664133/SRR7664133"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664134/SRR7664134"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664135/SRR7664135"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664136/SRR7664136"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664126/SRR7664126"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664128/SRR7664128"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664123/SRR7664123"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664124/SRR7664124"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664133/SRR7664133"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664135/SRR7664135"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664130/SRR7664130"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664132/SRR7664132"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664127/SRR7664127"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664129/SRR7664129"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664134/SRR7664134"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664136/SRR7664136"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664131/SRR7664131"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7664125/SRR7664125"

echo "Download complete. Files saved to $OUTDIR"