#!/usr/bin/env bash
# Bulk download script for GSE112782
# Generated from Yeo Lab Publications Database
# Total files: 23

OUTDIR="GSE112782"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112782/suppl/GSE112782_RAW.tar" -O "GSE112782_RAW.tar"

# --- 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 "SRR6950636"
gz1="$(_compress_if_exists 'SRR6950636_1' || true)"
gz2="$(_compress_if_exists 'SRR6950636_2' || true)"
gzs="$(_compress_if_exists 'SRR6950636' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_DX6Ai_S97_L007_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_DX6Ai_S97_L007_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950637"
gz1="$(_compress_if_exists 'SRR6950637_1' || true)"
gz2="$(_compress_if_exists 'SRR6950637_2' || true)"
gzs="$(_compress_if_exists 'SRR6950637' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_DX6Bi_S99_L007_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_DX6Bi_S99_L007_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950638"
gz1="$(_compress_if_exists 'SRR6950638_1' || true)"
gz2="$(_compress_if_exists 'SRR6950638_2' || true)"
gzs="$(_compress_if_exists 'SRR6950638' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_DX6A_S98_L007_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_DX6A_S98_L007_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950639"
gz1="$(_compress_if_exists 'SRR6950639_1' || true)"
gz2="$(_compress_if_exists 'SRR6950639_2' || true)"
gzs="$(_compress_if_exists 'SRR6950639' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SA_DX6B_S100_L007_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "SA_DX6B_S100_L007_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950640"
gz1="$(_compress_if_exists 'SRR6950640_1' || true)"
gz2="$(_compress_if_exists 'SRR6950640_2' || true)"
gzs="$(_compress_if_exists 'SRR6950640' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EY_INPUT_ILF2_H1_S3_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950641"
gz1="$(_compress_if_exists 'SRR6950641_1' || true)"
gz2="$(_compress_if_exists 'SRR6950641_2' || true)"
gzs="$(_compress_if_exists 'SRR6950641' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EY_INPUT_FUS_H1_S1_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950642"
gz1="$(_compress_if_exists 'SRR6950642_1' || true)"
gz2="$(_compress_if_exists 'SRR6950642_2' || true)"
gzs="$(_compress_if_exists 'SRR6950642' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EY_INPUT_DCP1B_H1_S2_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950643"
gz1="$(_compress_if_exists 'SRR6950643_1' || true)"
gz2="$(_compress_if_exists 'SRR6950643_2' || true)"
gzs="$(_compress_if_exists 'SRR6950643' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EY_IP_ILF2_H1_S6_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950644"
gz1="$(_compress_if_exists 'SRR6950644_1' || true)"
gz2="$(_compress_if_exists 'SRR6950644_2' || true)"
gzs="$(_compress_if_exists 'SRR6950644' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EY_IP_FUS_H1_S4_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR6950645"
gz1="$(_compress_if_exists 'SRR6950645_1' || true)"
gz2="$(_compress_if_exists 'SRR6950645_2' || true)"
gzs="$(_compress_if_exists 'SRR6950645' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "EY_IP_DCP1B_H1_S5_L006_R1_001.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950636/SRR6950636"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950637/SRR6950637"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950638/SRR6950638"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950639/SRR6950639"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950640/SRR6950640"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950641/SRR6950641"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950642/SRR6950642"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950643/SRR6950643"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950644/SRR6950644"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950645/SRR6950645"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950642/SRR6950642"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950641/SRR6950641"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950640/SRR6950640"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950645/SRR6950645"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950644/SRR6950644"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950643/SRR6950643"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950636/SRR6950636"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950638/SRR6950638"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950637/SRR6950637"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950639/SRR6950639"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950639/SRR6950639"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6950641/SRR6950641"

echo "Download complete. Files saved to $OUTDIR"