#!/usr/bin/env bash
# Bulk download script for GSE273093
# Generated from Yeo Lab Publications Database
# Total files: 14

OUTDIR="GSE273093"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE273nnn/GSE273093/suppl/GSE273093_featureCounts_output.txt.gz" -O "GSE273093_featureCounts_output.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE273nnn/GSE273093/suppl/GSE273093_myotubes_zfp697_deseq2.txt.gz" -O "GSE273093_myotubes_zfp697_deseq2.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 "SRR29988484"
gz1="$(_compress_if_exists 'SRR29988484_1' || true)"
gz2="$(_compress_if_exists 'SRR29988484_2' || true)"
gzs="$(_compress_if_exists 'SRR29988484' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "Zfp697_3.fastq.gz"
fi

fasterq-dump --split-files "SRR29988485"
gz1="$(_compress_if_exists 'SRR29988485_1' || true)"
gz2="$(_compress_if_exists 'SRR29988485_2' || true)"
gzs="$(_compress_if_exists 'SRR29988485' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Zfp697_2.fastq.gz"
fi

fasterq-dump --split-files "SRR29988486"
gz1="$(_compress_if_exists 'SRR29988486_1' || true)"
gz2="$(_compress_if_exists 'SRR29988486_2' || true)"
gzs="$(_compress_if_exists 'SRR29988486' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Zfp697_1.fastq.gz"
fi

fasterq-dump --split-files "SRR29988487"
gz1="$(_compress_if_exists 'SRR29988487_1' || true)"
gz2="$(_compress_if_exists 'SRR29988487_2' || true)"
gzs="$(_compress_if_exists 'SRR29988487' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "GFP_3.fastq.gz"
fi

fasterq-dump --split-files "SRR29988488"
gz1="$(_compress_if_exists 'SRR29988488_1' || true)"
gz2="$(_compress_if_exists 'SRR29988488_2' || true)"
gzs="$(_compress_if_exists 'SRR29988488' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "GFP_2.fastq.gz"
fi

fasterq-dump --split-files "SRR29988489"
gz1="$(_compress_if_exists 'SRR29988489_1' || true)"
gz2="$(_compress_if_exists 'SRR29988489_2' || true)"
gzs="$(_compress_if_exists 'SRR29988489' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "GFP_1.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988484/SRR29988484"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988485/SRR29988485"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988486/SRR29988486"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988487/SRR29988487"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988488/SRR29988488"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988489/SRR29988489"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988489/SRR29988489"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988488/SRR29988488"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988487/SRR29988487"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988486/SRR29988486"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988485/SRR29988485"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29988484/SRR29988484"

echo "Download complete. Files saved to $OUTDIR"