#!/usr/bin/env bash
# Bulk download script for GSE302648
# Generated from Yeo Lab Knowledgebase
# Total files: 19

OUTDIR=GSE302648
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE302nnn/GSE302648/suppl/GSE302648_input_RNA_vs_RIP_seq_counts_and_DESeq2_results.csv.gz -O GSE302648_input_RNA_vs_RIP_seq_counts_and_DESeq2_results.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 SRR34546509
gz1="$(_compress_if_exists SRR34546509_1 || true)"
gz2="$(_compress_if_exists SRR34546509_2 || true)"
gzs="$(_compress_if_exists SRR34546509 || true)"

fasterq-dump --split-files SRR34546510
gz1="$(_compress_if_exists SRR34546510_1 || true)"
gz2="$(_compress_if_exists SRR34546510_2 || true)"
gzs="$(_compress_if_exists SRR34546510 || true)"

fasterq-dump --split-files SRR34546511
gz1="$(_compress_if_exists SRR34546511_1 || true)"
gz2="$(_compress_if_exists SRR34546511_2 || true)"
gzs="$(_compress_if_exists SRR34546511 || true)"

fasterq-dump --split-files SRR34546512
gz1="$(_compress_if_exists SRR34546512_1 || true)"
gz2="$(_compress_if_exists SRR34546512_2 || true)"
gzs="$(_compress_if_exists SRR34546512 || true)"

fasterq-dump --split-files SRR34546513
gz1="$(_compress_if_exists SRR34546513_1 || true)"
gz2="$(_compress_if_exists SRR34546513_2 || true)"
gzs="$(_compress_if_exists SRR34546513 || true)"

fasterq-dump --split-files SRR34546514
gz1="$(_compress_if_exists SRR34546514_1 || true)"
gz2="$(_compress_if_exists SRR34546514_2 || true)"
gzs="$(_compress_if_exists SRR34546514 || true)"

fasterq-dump --split-files SRR34546515
gz1="$(_compress_if_exists SRR34546515_1 || true)"
gz2="$(_compress_if_exists SRR34546515_2 || true)"
gzs="$(_compress_if_exists SRR34546515 || true)"

fasterq-dump --split-files SRR34546516
gz1="$(_compress_if_exists SRR34546516_1 || true)"
gz2="$(_compress_if_exists SRR34546516_2 || true)"
gzs="$(_compress_if_exists SRR34546516 || true)"

fasterq-dump --split-files SRR34546517
gz1="$(_compress_if_exists SRR34546517_1 || true)"
gz2="$(_compress_if_exists SRR34546517_2 || true)"
gzs="$(_compress_if_exists SRR34546517 || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546509/SRR34546509.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546510/SRR34546510.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546511/SRR34546511.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546512/SRR34546512.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546513/SRR34546513.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546514/SRR34546514.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546515/SRR34546515.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546516/SRR34546516.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546517/SRR34546517.lite.1

# --- Additional data files ---
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546509/SRR34546509.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546510/SRR34546510.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546511/SRR34546511.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546512/SRR34546512.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546513/SRR34546513.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546514/SRR34546514.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546515/SRR34546515.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546516/SRR34546516.lite.1
curl -L -O -C - https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR034/34546/SRR34546517/SRR34546517.lite.1

echo "Download complete. Files saved to $OUTDIR"