#!/usr/bin/env bash
# Bulk download script for GSE122425
# Generated from Yeo Lab Publications Database
# Total files: 14

OUTDIR="GSE122425"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122425/suppl/GSE122425_Group_293-VS-293-NK_DE_significant_anno.xlsx" -O "GSE122425_Group_293-VS-293-NK_DE_significant_anno.xlsx"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122425/suppl/GSE122425_all.counts.293_vs_293NK.edgeR_all.xls.gz" -O "GSE122425_all.counts.293_vs_293NK.edgeR_all.xls.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 "SRR8181090"
gz1="$(_compress_if_exists 'SRR8181090_1' || true)"
gz2="$(_compress_if_exists 'SRR8181090_2' || true)"
gzs="$(_compress_if_exists 'SRR8181090' || true)"

fasterq-dump --split-files "SRR8181091"
gz1="$(_compress_if_exists 'SRR8181091_1' || true)"
gz2="$(_compress_if_exists 'SRR8181091_2' || true)"
gzs="$(_compress_if_exists 'SRR8181091' || true)"

fasterq-dump --split-files "SRR8181092"
gz1="$(_compress_if_exists 'SRR8181092_1' || true)"
gz2="$(_compress_if_exists 'SRR8181092_2' || true)"
gzs="$(_compress_if_exists 'SRR8181092' || true)"

fasterq-dump --split-files "SRR8181093"
gz1="$(_compress_if_exists 'SRR8181093_1' || true)"
gz2="$(_compress_if_exists 'SRR8181093_2' || true)"
gzs="$(_compress_if_exists 'SRR8181093' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "HEK293NK-SEQ1_combined_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "HEK293NK-SEQ1_combined_R2.fastq.gz"
fi

fasterq-dump --split-files "SRR8181094"
gz1="$(_compress_if_exists 'SRR8181094_1' || true)"
gz2="$(_compress_if_exists 'SRR8181094_2' || true)"
gzs="$(_compress_if_exists 'SRR8181094' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "HEK293NK-SEQ2_combined_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "HEK293NK-SEQ2_combined_R2.fastq.gz"
fi

fasterq-dump --split-files "SRR8181095"
gz1="$(_compress_if_exists 'SRR8181095_1' || true)"
gz2="$(_compress_if_exists 'SRR8181095_2' || true)"
gzs="$(_compress_if_exists 'SRR8181095' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "HEK293NK-SEQ3_combined_R1.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "HEK293NK-SEQ3_combined_R2.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181090/SRR8181090"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181091/SRR8181091"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181092/SRR8181092"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181093/SRR8181093"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181094/SRR8181094"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181095/SRR8181095"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181093/SRR8181093"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181094/SRR8181094"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181095/SRR8181095"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181090/SRR8181090"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181091/SRR8181091"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8181092/SRR8181092"

echo "Download complete. Files saved to $OUTDIR"