#!/usr/bin/env bash
# Bulk download script for GSE136910
# Generated from Yeo Lab Publications Database
# Total files: 20

OUTDIR="GSE136910"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE136nnn/GSE136910/suppl/GSE136910_RAW.tar" -O "GSE136910_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 "SRR10071341"
gz1="$(_compress_if_exists 'SRR10071341_1' || true)"
gz2="$(_compress_if_exists 'SRR10071341_2' || true)"
gzs="$(_compress_if_exists 'SRR10071341' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WT_1_SAT_S26_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WT_1_SAT_S26_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071342"
gz1="$(_compress_if_exists 'SRR10071342_1' || true)"
gz2="$(_compress_if_exists 'SRR10071342_2' || true)"
gzs="$(_compress_if_exists 'SRR10071342' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WT_2_SAT_S23_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WT_2_SAT_S23_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071343"
gz1="$(_compress_if_exists 'SRR10071343_1' || true)"
gz2="$(_compress_if_exists 'SRR10071343_2' || true)"
gzs="$(_compress_if_exists 'SRR10071343' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WT_3_SAT_S20_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WT_3_SAT_S20_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071344"
gz1="$(_compress_if_exists 'SRR10071344_1' || true)"
gz2="$(_compress_if_exists 'SRR10071344_2' || true)"
gzs="$(_compress_if_exists 'SRR10071344' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "AGO_1_Hete_SAT_S21_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "AGO_1_Hete_SAT_S21_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071345"
gz1="$(_compress_if_exists 'SRR10071345_1' || true)"
gz2="$(_compress_if_exists 'SRR10071345_2' || true)"
gzs="$(_compress_if_exists 'SRR10071345' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "AGO_2_Hete_SAT_S24_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "AGO_2_Hete_SAT_S24_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071346"
gz1="$(_compress_if_exists 'SRR10071346_1' || true)"
gz2="$(_compress_if_exists 'SRR10071346_2' || true)"
gzs="$(_compress_if_exists 'SRR10071346' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "AGO_3_Hete_SAT_S27_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "AGO_3_Hete_SAT_S27_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071347"
gz1="$(_compress_if_exists 'SRR10071347_1' || true)"
gz2="$(_compress_if_exists 'SRR10071347_2' || true)"
gzs="$(_compress_if_exists 'SRR10071347' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "AGO_1_Homo_SAT_S19_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "AGO_1_Homo_SAT_S19_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071348"
gz1="$(_compress_if_exists 'SRR10071348_1' || true)"
gz2="$(_compress_if_exists 'SRR10071348_2' || true)"
gzs="$(_compress_if_exists 'SRR10071348' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "AGO_2_Homo_SAT_S25_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "AGO_2_Homo_SAT_S25_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR10071349"
gz1="$(_compress_if_exists 'SRR10071349_1' || true)"
gz2="$(_compress_if_exists 'SRR10071349_2' || true)"
gzs="$(_compress_if_exists 'SRR10071349' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "AGO_3_Homo_SAT_S22_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "AGO_3_Homo_SAT_S22_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/SRR10071341/SRR10071341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071342/SRR10071342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071343/SRR10071343"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071344/SRR10071344"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071345/SRR10071345"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071346/SRR10071346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071347/SRR10071347"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071348/SRR10071348"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071349/SRR10071349"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071344/SRR10071344"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071347/SRR10071347"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071345/SRR10071345"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071348/SRR10071348"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071346/SRR10071346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071349/SRR10071349"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071346/SRR10071346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071341/SRR10071341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071342/SRR10071342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10071343/SRR10071343"

echo "Download complete. Files saved to $OUTDIR"