#!/usr/bin/env bash
# Bulk download script for GSE149767
# Generated from Yeo Lab Publications Database
# Total files: 101

OUTDIR="GSE149767"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_293t_vitro_icshape.tar.gz" -O "GSE149767_293t_vitro_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_293t_vivo_icshape.tar.gz" -O "GSE149767_293t_vivo_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_293tmaps.tar.gz" -O "GSE149767_293tmaps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_dms_shapeclip_maps.tar.gz" -O "GSE149767_dms_shapeclip_maps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_fshape_clip_maps.tar.gz" -O "GSE149767_fshape_clip_maps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_hela_vitro_icshape.tar.gz" -O "GSE149767_hela_vitro_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_hela_vivo_icshape.tar.gz" -O "GSE149767_hela_vivo_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_helamaps.tar.gz" -O "GSE149767_helamaps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_hepg2_vitro_icshape.tar.gz" -O "GSE149767_hepg2_vitro_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_hepg2_vivo_icshape.tar.gz" -O "GSE149767_hepg2_vivo_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_hepg2maps.tar.gz" -O "GSE149767_hepg2maps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_k562_vitro_icshape.tar.gz" -O "GSE149767_k562_vitro_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_k562_vivo_icshape.tar.gz" -O "GSE149767_k562_vivo_icshape.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_k562maps.tar.gz" -O "GSE149767_k562maps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_nai_shapeclip_maps.tar.gz" -O "GSE149767_nai_shapeclip_maps.tar.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_nodms_reproducible_peaks.hg38.bed.gz" -O "GSE149767_nodms_reproducible_peaks.hg38.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_nonai_reproducible_peaks.hg38.bed.gz" -O "GSE149767_nonai_reproducible_peaks.hg38.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_readme.txt" -O "GSE149767_readme.txt"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_vitro_reproducible_peaks.hg38.bed.gz" -O "GSE149767_vitro_reproducible_peaks.hg38.bed.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE149nnn/GSE149767/suppl/GSE149767_vivo_reproducible_peaks.hg38.bed.gz" -O "GSE149767_vivo_reproducible_peaks.hg38.bed.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 "SRR11682352"
gz1="$(_compress_if_exists 'SRR11682352_1' || true)"
gz2="$(_compress_if_exists 'SRR11682352_2' || true)"
gzs="$(_compress_if_exists 'SRR11682352' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "K562_vivo_N1.fastq.gz"
fi

fasterq-dump --split-files "SRR11682353"
gz1="$(_compress_if_exists 'SRR11682353_1' || true)"
gz2="$(_compress_if_exists 'SRR11682353_2' || true)"
gzs="$(_compress_if_exists 'SRR11682353' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "K562_vivo_N2.fastq.gz"
fi

fasterq-dump --split-files "SRR11682354"
gz1="$(_compress_if_exists 'SRR11682354_1' || true)"
gz2="$(_compress_if_exists 'SRR11682354_2' || true)"
gzs="$(_compress_if_exists 'SRR11682354' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "K562_vitro_N1.fastq.gz"
fi

fasterq-dump --split-files "SRR11682355"
gz1="$(_compress_if_exists 'SRR11682355_1' || true)"
gz2="$(_compress_if_exists 'SRR11682355_2' || true)"
gzs="$(_compress_if_exists 'SRR11682355' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "K562_vitro_N2.fastq.gz"
fi

fasterq-dump --split-files "SRR11682356"
gz1="$(_compress_if_exists 'SRR11682356_1' || true)"
gz2="$(_compress_if_exists 'SRR11682356_2' || true)"
gzs="$(_compress_if_exists 'SRR11682356' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HepG2_vivo_N1.fastq.gz"
fi

fasterq-dump --split-files "SRR11682357"
gz1="$(_compress_if_exists 'SRR11682357_1' || true)"
gz2="$(_compress_if_exists 'SRR11682357_2' || true)"
gzs="$(_compress_if_exists 'SRR11682357' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HepG2_vivo_N2.fastq.gz"
fi

fasterq-dump --split-files "SRR11682358"
gz1="$(_compress_if_exists 'SRR11682358_1' || true)"
gz2="$(_compress_if_exists 'SRR11682358_2' || true)"
gzs="$(_compress_if_exists 'SRR11682358' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HepG2_vitro_N1.fastq.gz"
fi

fasterq-dump --split-files "SRR11682359"
gz1="$(_compress_if_exists 'SRR11682359_1' || true)"
gz2="$(_compress_if_exists 'SRR11682359_2' || true)"
gzs="$(_compress_if_exists 'SRR11682359' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HepG2_vitro_N2.fastq.gz"
fi

fasterq-dump --split-files "SRR11682360"
gz1="$(_compress_if_exists 'SRR11682360_1' || true)"
gz2="$(_compress_if_exists 'SRR11682360_2' || true)"
gzs="$(_compress_if_exists 'SRR11682360' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HeLa_vivo_N1.fastq.gz"
fi

fasterq-dump --split-files "SRR11682361"
gz1="$(_compress_if_exists 'SRR11682361_1' || true)"
gz2="$(_compress_if_exists 'SRR11682361_2' || true)"
gzs="$(_compress_if_exists 'SRR11682361' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HeLa_vivo_N2.fastq.gz"
fi

fasterq-dump --split-files "SRR11682362"
gz1="$(_compress_if_exists 'SRR11682362_1' || true)"
gz2="$(_compress_if_exists 'SRR11682362_2' || true)"
gzs="$(_compress_if_exists 'SRR11682362' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HeLa_vitro_N1.fastq.gz"
fi

fasterq-dump --split-files "SRR11682363"
gz1="$(_compress_if_exists 'SRR11682363_1' || true)"
gz2="$(_compress_if_exists 'SRR11682363_2' || true)"
gzs="$(_compress_if_exists 'SRR11682363' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HeLa_vitro_N2.fastq.gz"
fi

fasterq-dump --split-files "SRR11682364"
gz1="$(_compress_if_exists 'SRR11682364_1' || true)"
gz2="$(_compress_if_exists 'SRR11682364_2' || true)"
gzs="$(_compress_if_exists 'SRR11682364' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noDMS1_IP_S53_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682365"
gz1="$(_compress_if_exists 'SRR11682365_1' || true)"
gz2="$(_compress_if_exists 'SRR11682365_2' || true)"
gzs="$(_compress_if_exists 'SRR11682365' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noDMS2_IP_S55_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682366"
gz1="$(_compress_if_exists 'SRR11682366_1' || true)"
gz2="$(_compress_if_exists 'SRR11682366_2' || true)"
gzs="$(_compress_if_exists 'SRR11682366' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noDMS1_Input_S52_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682367"
gz1="$(_compress_if_exists 'SRR11682367_1' || true)"
gz2="$(_compress_if_exists 'SRR11682367_2' || true)"
gzs="$(_compress_if_exists 'SRR11682367' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noDMS2_Input_S54_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682368"
gz1="$(_compress_if_exists 'SRR11682368_1' || true)"
gz2="$(_compress_if_exists 'SRR11682368_2' || true)"
gzs="$(_compress_if_exists 'SRR11682368' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_DMS1_IP_S49_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682369"
gz1="$(_compress_if_exists 'SRR11682369_1' || true)"
gz2="$(_compress_if_exists 'SRR11682369_2' || true)"
gzs="$(_compress_if_exists 'SRR11682369' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_DMS2_IP_S51_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682370"
gz1="$(_compress_if_exists 'SRR11682370_1' || true)"
gz2="$(_compress_if_exists 'SRR11682370_2' || true)"
gzs="$(_compress_if_exists 'SRR11682370' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_DMS1_Input_S48_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682371"
gz1="$(_compress_if_exists 'SRR11682371_1' || true)"
gz2="$(_compress_if_exists 'SRR11682371_2' || true)"
gzs="$(_compress_if_exists 'SRR11682371' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_DMS2_Input_S50_L004_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682372"
gz1="$(_compress_if_exists 'SRR11682372_1' || true)"
gz2="$(_compress_if_exists 'SRR11682372_2' || true)"
gzs="$(_compress_if_exists 'SRR11682372' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noNAI1_IP_S1_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682373"
gz1="$(_compress_if_exists 'SRR11682373_1' || true)"
gz2="$(_compress_if_exists 'SRR11682373_2' || true)"
gzs="$(_compress_if_exists 'SRR11682373' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noNAI2_IP_S2_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682374"
gz1="$(_compress_if_exists 'SRR11682374_1' || true)"
gz2="$(_compress_if_exists 'SRR11682374_2' || true)"
gzs="$(_compress_if_exists 'SRR11682374' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noNAI1_Input_S3_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682375"
gz1="$(_compress_if_exists 'SRR11682375_1' || true)"
gz2="$(_compress_if_exists 'SRR11682375_2' || true)"
gzs="$(_compress_if_exists 'SRR11682375' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_noNAI2_Input_S4_L006_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682376"
gz1="$(_compress_if_exists 'SRR11682376_1' || true)"
gz2="$(_compress_if_exists 'SRR11682376_2' || true)"
gzs="$(_compress_if_exists 'SRR11682376' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_NAI1_IP_S31_L007_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682377"
gz1="$(_compress_if_exists 'SRR11682377_1' || true)"
gz2="$(_compress_if_exists 'SRR11682377_2' || true)"
gzs="$(_compress_if_exists 'SRR11682377' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_NAI2_IP_S55_L008_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682378"
gz1="$(_compress_if_exists 'SRR11682378_1' || true)"
gz2="$(_compress_if_exists 'SRR11682378_2' || true)"
gzs="$(_compress_if_exists 'SRR11682378' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vivo1_IP_S5_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682379"
gz1="$(_compress_if_exists 'SRR11682379_1' || true)"
gz2="$(_compress_if_exists 'SRR11682379_2' || true)"
gzs="$(_compress_if_exists 'SRR11682379' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vivo2_IP_S6_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682380"
gz1="$(_compress_if_exists 'SRR11682380_1' || true)"
gz2="$(_compress_if_exists 'SRR11682380_2' || true)"
gzs="$(_compress_if_exists 'SRR11682380' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vivo1_Input_S1_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682381"
gz1="$(_compress_if_exists 'SRR11682381_1' || true)"
gz2="$(_compress_if_exists 'SRR11682381_2' || true)"
gzs="$(_compress_if_exists 'SRR11682381' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vivo2_Input_S2_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682382"
gz1="$(_compress_if_exists 'SRR11682382_1' || true)"
gz2="$(_compress_if_exists 'SRR11682382_2' || true)"
gzs="$(_compress_if_exists 'SRR11682382' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vitro1_IP_S7_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682383"
gz1="$(_compress_if_exists 'SRR11682383_1' || true)"
gz2="$(_compress_if_exists 'SRR11682383_2' || true)"
gzs="$(_compress_if_exists 'SRR11682383' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vitro2_IP_S8_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682384"
gz1="$(_compress_if_exists 'SRR11682384_1' || true)"
gz2="$(_compress_if_exists 'SRR11682384_2' || true)"
gzs="$(_compress_if_exists 'SRR11682384' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vitro1_Input_S3_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR11682385"
gz1="$(_compress_if_exists 'SRR11682385_1' || true)"
gz2="$(_compress_if_exists 'SRR11682385_2' || true)"
gzs="$(_compress_if_exists 'SRR11682385' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "MC_vitro2_Input_S4_L002_R1_001.fastq.gz"
fi

fasterq-dump --split-files "SRR12668784"
gz1="$(_compress_if_exists 'SRR12668784_1' || true)"
gz2="$(_compress_if_exists 'SRR12668784_2' || true)"
gzs="$(_compress_if_exists 'SRR12668784' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "K562_D1.fastq.gz"
fi

fasterq-dump --split-files "SRR12668785"
gz1="$(_compress_if_exists 'SRR12668785_1' || true)"
gz2="$(_compress_if_exists 'SRR12668785_2' || true)"
gzs="$(_compress_if_exists 'SRR12668785' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "K562_D2.fastq.gz"
fi

fasterq-dump --split-files "SRR12668786"
gz1="$(_compress_if_exists 'SRR12668786_1' || true)"
gz2="$(_compress_if_exists 'SRR12668786_2' || true)"
gzs="$(_compress_if_exists 'SRR12668786' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HepG2_D1.fastq.gz"
fi

fasterq-dump --split-files "SRR12668787"
gz1="$(_compress_if_exists 'SRR12668787_1' || true)"
gz2="$(_compress_if_exists 'SRR12668787_2' || true)"
gzs="$(_compress_if_exists 'SRR12668787' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HepG2_D2.fastq.gz"
fi

fasterq-dump --split-files "SRR12668788"
gz1="$(_compress_if_exists 'SRR12668788_1' || true)"
gz2="$(_compress_if_exists 'SRR12668788_2' || true)"
gzs="$(_compress_if_exists 'SRR12668788' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HeLa_D1.fastq.gz"
fi

fasterq-dump --split-files "SRR12668789"
gz1="$(_compress_if_exists 'SRR12668789_1' || true)"
gz2="$(_compress_if_exists 'SRR12668789_2' || true)"
gzs="$(_compress_if_exists 'SRR12668789' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gzs" ]; then
  mv -f "$gzs" "HeLa_D2.fastq.gz"
fi


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682352/SRR11682352"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682353/SRR11682353"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682354/SRR11682354"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682355/SRR11682355"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682356/SRR11682356"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682357/SRR11682357"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682358/SRR11682358"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682359/SRR11682359"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682360/SRR11682360"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682361/SRR11682361"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682362/SRR11682362"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682363/SRR11682363"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682364/SRR11682364"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682365/SRR11682365"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682366/SRR11682366"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682367/SRR11682367"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682368/SRR11682368"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682369/SRR11682369"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682370/SRR11682370"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682371/SRR11682371"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682372/SRR11682372"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682373/SRR11682373"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682374/SRR11682374"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682375/SRR11682375"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682376/SRR11682376"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682377/SRR11682377"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682378/SRR11682378"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682379/SRR11682379"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682380/SRR11682380"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682381/SRR11682381"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682382/SRR11682382"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682383/SRR11682383"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682384/SRR11682384"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682385/SRR11682385"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668784/SRR12668784"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668785/SRR12668785"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668786/SRR12668786"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668787/SRR12668787"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668788/SRR12668788"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668789/SRR12668789"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668788/SRR12668788"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668789/SRR12668789"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682362/SRR11682362"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682363/SRR11682363"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682360/SRR11682360"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682361/SRR11682361"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668786/SRR12668786"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668787/SRR12668787"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682358/SRR11682358"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682359/SRR11682359"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682356/SRR11682356"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682357/SRR11682357"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668784/SRR12668784"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12668785/SRR12668785"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682354/SRR11682354"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682355/SRR11682355"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682352/SRR11682352"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682353/SRR11682353"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682370/SRR11682370"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682368/SRR11682368"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682371/SRR11682371"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682369/SRR11682369"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682376/SRR11682376"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682377/SRR11682377"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682366/SRR11682366"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682364/SRR11682364"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682367/SRR11682367"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682365/SRR11682365"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682374/SRR11682374"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682372/SRR11682372"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682375/SRR11682375"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682373/SRR11682373"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682384/SRR11682384"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682382/SRR11682382"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682385/SRR11682385"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682383/SRR11682383"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682380/SRR11682380"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682378/SRR11682378"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682381/SRR11682381"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11682379/SRR11682379"
curl -L -O -C - "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos9/sra-pub-zq-924/SRR011/11682/SRR11682354/SRR11682354.lite.1"

echo "Download complete. Files saved to $OUTDIR"