#!/usr/bin/env bash
# Bulk download script for GSE195495
# Generated from Yeo Lab Publications Database
# Total files: 20

OUTDIR="GSE195495"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE195nnn/GSE195495/suppl/GSE195495_PABPCvInput_DE.csv.gz" -O "GSE195495_PABPCvInput_DE.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE195nnn/GSE195495/suppl/GSE195495_PABPNvInput_DE.csv.gz" -O "GSE195495_PABPNvInput_DE.csv.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 "SRR17771363"
gz1="$(_compress_if_exists 'SRR17771363_1' || true)"
gz2="$(_compress_if_exists 'SRR17771363_2' || true)"
gzs="$(_compress_if_exists 'SRR17771363' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RIP_PABPC_Rep3.fastq.gz"
fi

fasterq-dump --split-files "SRR17771364"
gz1="$(_compress_if_exists 'SRR17771364_1' || true)"
gz2="$(_compress_if_exists 'SRR17771364_2' || true)"
gzs="$(_compress_if_exists 'SRR17771364' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RIP_PABPC_Rep2.fastq.gz"
fi

fasterq-dump --split-files "SRR17771365"
gz1="$(_compress_if_exists 'SRR17771365_1' || true)"
gz2="$(_compress_if_exists 'SRR17771365_2' || true)"
gzs="$(_compress_if_exists 'SRR17771365' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RIP_PABPC_Rep1.fastq.gz"
fi

fasterq-dump --split-files "SRR17771366"
gz1="$(_compress_if_exists 'SRR17771366_1' || true)"
gz2="$(_compress_if_exists 'SRR17771366_2' || true)"
gzs="$(_compress_if_exists 'SRR17771366' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RIP_PABPN_Rep3.fastq.gz"
fi

fasterq-dump --split-files "SRR17771367"
gz1="$(_compress_if_exists 'SRR17771367_1' || true)"
gz2="$(_compress_if_exists 'SRR17771367_2' || true)"
gzs="$(_compress_if_exists 'SRR17771367' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RIP_PABPN_Rep2.fastq.gz"
fi

fasterq-dump --split-files "SRR17771368"
gz1="$(_compress_if_exists 'SRR17771368_1' || true)"
gz2="$(_compress_if_exists 'SRR17771368_2' || true)"
gzs="$(_compress_if_exists 'SRR17771368' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "RIP_PABPN_Rep1.fastq.gz"
fi

fasterq-dump --split-files "SRR17771369"
gz1="$(_compress_if_exists 'SRR17771369_1' || true)"
gz2="$(_compress_if_exists 'SRR17771369_2' || true)"
gzs="$(_compress_if_exists 'SRR17771369' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "TotalInput_Rep3.fastq.gz"
fi

fasterq-dump --split-files "SRR17771370"
gz1="$(_compress_if_exists 'SRR17771370_1' || true)"
gz2="$(_compress_if_exists 'SRR17771370_2' || true)"
gzs="$(_compress_if_exists 'SRR17771370' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "TotalInput_Rep2.fastq.gz"
fi

fasterq-dump --split-files "SRR17771371"
gz1="$(_compress_if_exists 'SRR17771371_1' || true)"
gz2="$(_compress_if_exists 'SRR17771371_2' || true)"
gzs="$(_compress_if_exists 'SRR17771371' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "TotalInput_Rep1.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771363/SRR17771363"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771364/SRR17771364"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771365/SRR17771365"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771366/SRR17771366"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771367/SRR17771367"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771368/SRR17771368"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771369/SRR17771369"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771370/SRR17771370"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771371/SRR17771371"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771365/SRR17771365"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771364/SRR17771364"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771363/SRR17771363"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771368/SRR17771368"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771367/SRR17771367"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771366/SRR17771366"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771371/SRR17771371"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771370/SRR17771370"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17771369/SRR17771369"

echo "Download complete. Files saved to $OUTDIR"