#!/usr/bin/env bash
# Bulk download script for GSE122069
# Generated from Yeo Lab Publications Database
# Total files: 21

OUTDIR="GSE122069"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122069/suppl/GSE122069_RSEM.gene.TPM.txt.gz" -O "GSE122069_RSEM.gene.TPM.txt.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 "SRR8144907"
gz1="$(_compress_if_exists 'SRR8144907_1' || true)"
gz2="$(_compress_if_exists 'SRR8144907_2' || true)"
gzs="$(_compress_if_exists 'SRR8144907' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SiC_1.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144908"
gz1="$(_compress_if_exists 'SRR8144908_1' || true)"
gz2="$(_compress_if_exists 'SRR8144908_2' || true)"
gzs="$(_compress_if_exists 'SRR8144908' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SiC_2.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144909"
gz1="$(_compress_if_exists 'SRR8144909_1' || true)"
gz2="$(_compress_if_exists 'SRR8144909_2' || true)"
gzs="$(_compress_if_exists 'SRR8144909' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "SiC_3.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144910"
gz1="$(_compress_if_exists 'SRR8144910_1' || true)"
gz2="$(_compress_if_exists 'SRR8144910_2' || true)"
gzs="$(_compress_if_exists 'SRR8144910' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SiT_1.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144911"
gz1="$(_compress_if_exists 'SRR8144911_1' || true)"
gz2="$(_compress_if_exists 'SRR8144911_2' || true)"
gzs="$(_compress_if_exists 'SRR8144911' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SiT_2.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144912"
gz1="$(_compress_if_exists 'SRR8144912_1' || true)"
gz2="$(_compress_if_exists 'SRR8144912_2' || true)"
gzs="$(_compress_if_exists 'SRR8144912' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "SiT_3.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144913"
gz1="$(_compress_if_exists 'SRR8144913_1' || true)"
gz2="$(_compress_if_exists 'SRR8144913_2' || true)"
gzs="$(_compress_if_exists 'SRR8144913' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "79.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144914"
gz1="$(_compress_if_exists 'SRR8144914_1' || true)"
gz2="$(_compress_if_exists 'SRR8144914_2' || true)"
gzs="$(_compress_if_exists 'SRR8144914' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "80.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144915"
gz1="$(_compress_if_exists 'SRR8144915_1' || true)"
gz2="$(_compress_if_exists 'SRR8144915_2' || true)"
gzs="$(_compress_if_exists 'SRR8144915' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "81.fastq.bz2.gz"
fi

fasterq-dump --split-files "SRR8144916"
gz1="$(_compress_if_exists 'SRR8144916_1' || true)"
gz2="$(_compress_if_exists 'SRR8144916_2' || true)"
gzs="$(_compress_if_exists 'SRR8144916' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "82.fastq.bz2.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144907/SRR8144907"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144908/SRR8144908"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144909/SRR8144909"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144910/SRR8144910"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144911/SRR8144911"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144912/SRR8144912"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144913/SRR8144913"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144914/SRR8144914"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144915/SRR8144915"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144916/SRR8144916"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144913/SRR8144913"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144914/SRR8144914"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144915/SRR8144915"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144916/SRR8144916"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144907/SRR8144907"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144908/SRR8144908"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144909/SRR8144909"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144910/SRR8144910"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144911/SRR8144911"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8144912/SRR8144912"

echo "Download complete. Files saved to $OUTDIR"