#!/usr/bin/env bash
# Bulk download script for GSE146014
# Generated from Yeo Lab Publications Database
# Total files: 15

OUTDIR="GSE146014"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146014/suppl/GSE146014_tumor_colon.txt.gz" -O "GSE146014_tumor_colon.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 "SRR11211654"
gz1="$(_compress_if_exists 'SRR11211654_1' || true)"
gz2="$(_compress_if_exists 'SRR11211654_2' || true)"
gzs="$(_compress_if_exists 'SRR11211654' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "1555_Tumor_S5_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "1555_Tumor_S5_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11211655"
gz1="$(_compress_if_exists 'SRR11211655_1' || true)"
gz2="$(_compress_if_exists 'SRR11211655_2' || true)"
gzs="$(_compress_if_exists 'SRR11211655' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "1998_Tumor_S7_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "1998_Tumor_S7_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11211656"
gz1="$(_compress_if_exists 'SRR11211656_1' || true)"
gz2="$(_compress_if_exists 'SRR11211656_2' || true)"
gzs="$(_compress_if_exists 'SRR11211656' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "2070_Tumor_S9_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "2070_Tumor_S9_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11211657"
gz1="$(_compress_if_exists 'SRR11211657_1' || true)"
gz2="$(_compress_if_exists 'SRR11211657_2' || true)"
gzs="$(_compress_if_exists 'SRR11211657' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "1553_Tumor_S6_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "1553_Tumor_S6_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11211658"
gz1="$(_compress_if_exists 'SRR11211658_1' || true)"
gz2="$(_compress_if_exists 'SRR11211658_2' || true)"
gzs="$(_compress_if_exists 'SRR11211658' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "1995_Tumor_S8_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "1995_Tumor_S8_L004_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11211659"
gz1="$(_compress_if_exists 'SRR11211659_1' || true)"
gz2="$(_compress_if_exists 'SRR11211659_2' || true)"
gzs="$(_compress_if_exists 'SRR11211659' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "2072_Tumor_S10_L004_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "2072_Tumor_S10_L004_R2_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211654/SRR11211654"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211655/SRR11211655"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211656/SRR11211656"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211657/SRR11211657"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211658/SRR11211658"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211659/SRR11211659"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211657/SRR11211657"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211654/SRR11211654"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211658/SRR11211658"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211655/SRR11211655"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211656/SRR11211656"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11211659/SRR11211659"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR011/11211/SRR11211654/SRR11211654.lite.1"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-1/SRR011/11211/SRR11211656/SRR11211656.lite.1"

echo "Download complete. Files saved to $OUTDIR"