#!/usr/bin/env bash
# Bulk download script for GSE217735
# Generated from Yeo Lab Publications Database
# Total files: 13

OUTDIR="GSE217735"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE217nnn/GSE217735/suppl/GSE217735_NPC_Upf2KO_SZ20210524JZ.count.txt.gz" -O "GSE217735_NPC_Upf2KO_SZ20210524JZ.count.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 "SRR22255533"
gz1="$(_compress_if_exists 'SRR22255533_1' || true)"
gz2="$(_compress_if_exists 'SRR22255533_2' || true)"
gzs="$(_compress_if_exists 'SRR22255533' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_sgRNA_S52_L999_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR22255534"
gz1="$(_compress_if_exists 'SRR22255534_1' || true)"
gz2="$(_compress_if_exists 'SRR22255534_2' || true)"
gzs="$(_compress_if_exists 'SRR22255534' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_GFP_S53_L999_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR22255535"
gz1="$(_compress_if_exists 'SRR22255535_1' || true)"
gz2="$(_compress_if_exists 'SRR22255535_2' || true)"
gzs="$(_compress_if_exists 'SRR22255535' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_50_Cre_S54_L999_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR22255536"
gz1="$(_compress_if_exists 'SRR22255536_1' || true)"
gz2="$(_compress_if_exists 'SRR22255536_2' || true)"
gzs="$(_compress_if_exists 'SRR22255536' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_sgRNA_S49_L999_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR22255537"
gz1="$(_compress_if_exists 'SRR22255537_1' || true)"
gz2="$(_compress_if_exists 'SRR22255537_2' || true)"
gzs="$(_compress_if_exists 'SRR22255537' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_GFP_S50_L999_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR22255538"
gz1="$(_compress_if_exists 'SRR22255538_1' || true)"
gz2="$(_compress_if_exists 'SRR22255538_2' || true)"
gzs="$(_compress_if_exists 'SRR22255538' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "SZ20210524JZ_msEpiCRISPRi_NPC_Upf2KO_05_Cre_S51_L999_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/SRR22255533/SRR22255533"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255534/SRR22255534"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255535/SRR22255535"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255536/SRR22255536"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255537/SRR22255537"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255538/SRR22255538"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255538/SRR22255538"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255537/SRR22255537"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255536/SRR22255536"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255535/SRR22255535"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255534/SRR22255534"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22255533/SRR22255533"

echo "Download complete. Files saved to $OUTDIR"