#!/usr/bin/env bash
# Bulk download script for GSE230349
# Generated from Yeo Lab Publications Database
# Total files: 13

OUTDIR=GSE230349
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE230nnn/GSE230349/suppl/GSE230349_Riboseq_results_SerRS_overexpression.xlsx -O GSE230349_Riboseq_results_SerRS_overexpression.xlsx

# --- 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 SRR24267132
gz1="$(_compress_if_exists SRR24267132_1 || true)"
gz2="$(_compress_if_exists SRR24267132_2 || true)"
gzs="$(_compress_if_exists SRR24267132 || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" SLA_102.fastq.gz
fi

fasterq-dump --split-files SRR24267133
gz1="$(_compress_if_exists SRR24267133_1 || true)"
gz2="$(_compress_if_exists SRR24267133_2 || true)"
gzs="$(_compress_if_exists SRR24267133 || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" SLA_101.fastq.gz
fi

fasterq-dump --split-files SRR24267134
gz1="$(_compress_if_exists SRR24267134_1 || true)"
gz2="$(_compress_if_exists SRR24267134_2 || true)"
gzs="$(_compress_if_exists SRR24267134 || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" SLA_99.fastq.gz
fi

fasterq-dump --split-files SRR24267135
gz1="$(_compress_if_exists SRR24267135_1 || true)"
gz2="$(_compress_if_exists SRR24267135_2 || true)"
gzs="$(_compress_if_exists SRR24267135 || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" SLA_97.fastq.gz
fi

fasterq-dump --split-files SRR24267136
gz1="$(_compress_if_exists SRR24267136_1 || true)"
gz2="$(_compress_if_exists SRR24267136_2 || true)"
gzs="$(_compress_if_exists SRR24267136 || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" SLA_95.fastq.gz
fi

fasterq-dump --split-files SRR24267137
gz1="$(_compress_if_exists SRR24267137_1 || true)"
gz2="$(_compress_if_exists SRR24267137_2 || true)"
gzs="$(_compress_if_exists SRR24267137 || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" SLA_89.fastq.gz
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267132/SRR24267132
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267133/SRR24267133
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267134/SRR24267134
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267135/SRR24267135
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267136/SRR24267136
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267137/SRR24267137

# --- Additional data files ---
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267133/SRR24267133
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267132/SRR24267132
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267137/SRR24267137
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267136/SRR24267136
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267135/SRR24267135
curl -L -O -C - https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24267134/SRR24267134

echo "Download complete. Files saved to $OUTDIR"