#!/usr/bin/env bash
# Bulk download script for GSE123613
# Generated from Yeo Lab Publications Database
# Total files: 133

OUTDIR="GSE123613"
mkdir -p "$OUTDIR"
cd "$OUTDIR"

# --- GEO supplementary files ---
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_A3SS.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_A3SS.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_A5SS.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_A5SS.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_DEseq_PUS1KO_results.csv.gz" -O "GSE123613_DEseq_PUS1KO_results.csv.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_HepG2_IVT_pseudo-seq_pool.fasta.gz" -O "GSE123613_HepG2_IVT_pseudo-seq_pool.fasta.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_HepG2_prefs_newpkcall_v2_7reps_p1.0_l7.txt.gz" -O "GSE123613_HepG2_prefs_newpkcall_v2_7reps_p1.0_l7.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_MXE.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_MXE.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_PUS7.SE.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_PUS7.SE.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_PUS_Z-score.txt.gz" -O "GSE123613_PUS_Z-score.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_RI.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_RI.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_RPUSD4.SE.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_RPUSD4.SE.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_SE.MATS.JunctionCountOnly.txt.gz" -O "GSE123613_SE.MATS.JunctionCountOnly.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_rPUS_peaks_1.txt.gz" -O "GSE123613_rPUS_peaks_1.txt.gz"
wget -nc "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123613/suppl/GSE123613_rPUS_peaks_2.txt.gz" -O "GSE123613_rPUS_peaks_2.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 "SRR16967339"
gz1="$(_compress_if_exists 'SRR16967339_1' || true)"
gz2="$(_compress_if_exists 'SRR16967339_2' || true)"
gzs="$(_compress_if_exists 'SRR16967339' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WT1_S1_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WT1_S1_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967340"
gz1="$(_compress_if_exists 'SRR16967340_1' || true)"
gz2="$(_compress_if_exists 'SRR16967340_2' || true)"
gzs="$(_compress_if_exists 'SRR16967340' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "shPUS71_S1_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "shPUS71_S1_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967341"
gz1="$(_compress_if_exists 'SRR16967341_1' || true)"
gz2="$(_compress_if_exists 'SRR16967341_2' || true)"
gzs="$(_compress_if_exists 'SRR16967341' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WT2_S1_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WT2_S1_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967342"
gz1="$(_compress_if_exists 'SRR16967342_1' || true)"
gz2="$(_compress_if_exists 'SRR16967342_2' || true)"
gzs="$(_compress_if_exists 'SRR16967342' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "shPUS72_S1_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "shPUS72_S1_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967343"
gz1="$(_compress_if_exists 'SRR16967343_1' || true)"
gz2="$(_compress_if_exists 'SRR16967343_2' || true)"
gzs="$(_compress_if_exists 'SRR16967343' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "WT3_S1_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "WT3_S1_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967344"
gz1="$(_compress_if_exists 'SRR16967344_1' || true)"
gz2="$(_compress_if_exists 'SRR16967344_2' || true)"
gzs="$(_compress_if_exists 'SRR16967344' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "shPUS73_S1_L001_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "shPUS73_S1_L001_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967345"
gz1="$(_compress_if_exists 'SRR16967345_1' || true)"
gz2="$(_compress_if_exists 'SRR16967345_2' || true)"
gzs="$(_compress_if_exists 'SRR16967345' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Control-1-Resub_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Control-1-Resub_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967346"
gz1="$(_compress_if_exists 'SRR16967346_1' || true)"
gz2="$(_compress_if_exists 'SRR16967346_2' || true)"
gzs="$(_compress_if_exists 'SRR16967346' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "shRPUSD4-1-Resub_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "shRPUSD4-1-Resub_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967347"
gz1="$(_compress_if_exists 'SRR16967347_1' || true)"
gz2="$(_compress_if_exists 'SRR16967347_2' || true)"
gzs="$(_compress_if_exists 'SRR16967347' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "Control-2-Resub_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "Control-2-Resub_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR16967348"
gz1="$(_compress_if_exists 'SRR16967348_1' || true)"
gz2="$(_compress_if_exists 'SRR16967348_2' || true)"
gzs="$(_compress_if_exists 'SRR16967348' || true)"
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz1" ]; then
  mv -f "$gz1" "shRPUSD4-2-Resub_R1_001.fastq.gz"
fi
if [ "$RENAME_SRA_TO_ORIGINAL" = "1" ] && [ -n "$gz2" ]; then
  mv -f "$gz2" "shRPUSD4-2-Resub_R2_001.fastq.gz"
fi

fasterq-dump --split-files "SRR8311135"
gz1="$(_compress_if_exists 'SRR8311135_1' || true)"
gz2="$(_compress_if_exists 'SRR8311135_2' || true)"
gzs="$(_compress_if_exists 'SRR8311135' || true)"

fasterq-dump --split-files "SRR8311136"
gz1="$(_compress_if_exists 'SRR8311136_1' || true)"
gz2="$(_compress_if_exists 'SRR8311136_2' || true)"
gzs="$(_compress_if_exists 'SRR8311136' || true)"

fasterq-dump --split-files "SRR8311137"
gz1="$(_compress_if_exists 'SRR8311137_1' || true)"
gz2="$(_compress_if_exists 'SRR8311137_2' || true)"
gzs="$(_compress_if_exists 'SRR8311137' || true)"

fasterq-dump --split-files "SRR8311138"
gz1="$(_compress_if_exists 'SRR8311138_1' || true)"
gz2="$(_compress_if_exists 'SRR8311138_2' || true)"
gzs="$(_compress_if_exists 'SRR8311138' || true)"

fasterq-dump --split-files "SRR8311139"
gz1="$(_compress_if_exists 'SRR8311139_1' || true)"
gz2="$(_compress_if_exists 'SRR8311139_2' || true)"
gzs="$(_compress_if_exists 'SRR8311139' || true)"

fasterq-dump --split-files "SRR8311140"
gz1="$(_compress_if_exists 'SRR8311140_1' || true)"
gz2="$(_compress_if_exists 'SRR8311140_2' || true)"
gzs="$(_compress_if_exists 'SRR8311140' || true)"

fasterq-dump --split-files "SRR8311141"
gz1="$(_compress_if_exists 'SRR8311141_1' || true)"
gz2="$(_compress_if_exists 'SRR8311141_2' || true)"
gzs="$(_compress_if_exists 'SRR8311141' || true)"

fasterq-dump --split-files "SRR8311142"
gz1="$(_compress_if_exists 'SRR8311142_1' || true)"
gz2="$(_compress_if_exists 'SRR8311142_2' || true)"
gzs="$(_compress_if_exists 'SRR8311142' || true)"

fasterq-dump --split-files "SRR8311143"
gz1="$(_compress_if_exists 'SRR8311143_1' || true)"
gz2="$(_compress_if_exists 'SRR8311143_2' || true)"
gzs="$(_compress_if_exists 'SRR8311143' || true)"

fasterq-dump --split-files "SRR8311144"
gz1="$(_compress_if_exists 'SRR8311144_1' || true)"
gz2="$(_compress_if_exists 'SRR8311144_2' || true)"
gzs="$(_compress_if_exists 'SRR8311144' || true)"

fasterq-dump --split-files "SRR8311145"
gz1="$(_compress_if_exists 'SRR8311145_1' || true)"
gz2="$(_compress_if_exists 'SRR8311145_2' || true)"
gzs="$(_compress_if_exists 'SRR8311145' || true)"

fasterq-dump --split-files "SRR8311146"
gz1="$(_compress_if_exists 'SRR8311146_1' || true)"
gz2="$(_compress_if_exists 'SRR8311146_2' || true)"
gzs="$(_compress_if_exists 'SRR8311146' || true)"

fasterq-dump --split-files "SRR8311147"
gz1="$(_compress_if_exists 'SRR8311147_1' || true)"
gz2="$(_compress_if_exists 'SRR8311147_2' || true)"
gzs="$(_compress_if_exists 'SRR8311147' || true)"

fasterq-dump --split-files "SRR8311148"
gz1="$(_compress_if_exists 'SRR8311148_1' || true)"
gz2="$(_compress_if_exists 'SRR8311148_2' || true)"
gzs="$(_compress_if_exists 'SRR8311148' || true)"

fasterq-dump --split-files "SRR8311149"
gz1="$(_compress_if_exists 'SRR8311149_1' || true)"
gz2="$(_compress_if_exists 'SRR8311149_2' || true)"
gzs="$(_compress_if_exists 'SRR8311149' || true)"

fasterq-dump --split-files "SRR8311150"
gz1="$(_compress_if_exists 'SRR8311150_1' || true)"
gz2="$(_compress_if_exists 'SRR8311150_2' || true)"
gzs="$(_compress_if_exists 'SRR8311150' || true)"

fasterq-dump --split-files "SRR8311151"
gz1="$(_compress_if_exists 'SRR8311151_1' || true)"
gz2="$(_compress_if_exists 'SRR8311151_2' || true)"
gzs="$(_compress_if_exists 'SRR8311151' || true)"

fasterq-dump --split-files "SRR8311152"
gz1="$(_compress_if_exists 'SRR8311152_1' || true)"
gz2="$(_compress_if_exists 'SRR8311152_2' || true)"
gzs="$(_compress_if_exists 'SRR8311152' || true)"

fasterq-dump --split-files "SRR8311153"
gz1="$(_compress_if_exists 'SRR8311153_1' || true)"
gz2="$(_compress_if_exists 'SRR8311153_2' || true)"
gzs="$(_compress_if_exists 'SRR8311153' || true)"

fasterq-dump --split-files "SRR8311154"
gz1="$(_compress_if_exists 'SRR8311154_1' || true)"
gz2="$(_compress_if_exists 'SRR8311154_2' || true)"
gzs="$(_compress_if_exists 'SRR8311154' || true)"

fasterq-dump --split-files "SRR8311155"
gz1="$(_compress_if_exists 'SRR8311155_1' || true)"
gz2="$(_compress_if_exists 'SRR8311155_2' || true)"
gzs="$(_compress_if_exists 'SRR8311155' || true)"

fasterq-dump --split-files "SRR8311156"
gz1="$(_compress_if_exists 'SRR8311156_1' || true)"
gz2="$(_compress_if_exists 'SRR8311156_2' || true)"
gzs="$(_compress_if_exists 'SRR8311156' || true)"

fasterq-dump --split-files "SRR8311157"
gz1="$(_compress_if_exists 'SRR8311157_1' || true)"
gz2="$(_compress_if_exists 'SRR8311157_2' || true)"
gzs="$(_compress_if_exists 'SRR8311157' || true)"

fasterq-dump --split-files "SRR8311158"
gz1="$(_compress_if_exists 'SRR8311158_1' || true)"
gz2="$(_compress_if_exists 'SRR8311158_2' || true)"
gzs="$(_compress_if_exists 'SRR8311158' || true)"

fasterq-dump --split-files "SRR8311159"
gz1="$(_compress_if_exists 'SRR8311159_1' || true)"
gz2="$(_compress_if_exists 'SRR8311159_2' || true)"
gzs="$(_compress_if_exists 'SRR8311159' || true)"

fasterq-dump --split-files "SRR8311160"
gz1="$(_compress_if_exists 'SRR8311160_1' || true)"
gz2="$(_compress_if_exists 'SRR8311160_2' || true)"
gzs="$(_compress_if_exists 'SRR8311160' || true)"

fasterq-dump --split-files "SRR8311161"
gz1="$(_compress_if_exists 'SRR8311161_1' || true)"
gz2="$(_compress_if_exists 'SRR8311161_2' || true)"
gzs="$(_compress_if_exists 'SRR8311161' || true)"

fasterq-dump --split-files "SRR8311162"
gz1="$(_compress_if_exists 'SRR8311162_1' || true)"
gz2="$(_compress_if_exists 'SRR8311162_2' || true)"
gzs="$(_compress_if_exists 'SRR8311162' || true)"

fasterq-dump --split-files "SRR8311163"
gz1="$(_compress_if_exists 'SRR8311163_1' || true)"
gz2="$(_compress_if_exists 'SRR8311163_2' || true)"
gzs="$(_compress_if_exists 'SRR8311163' || true)"

fasterq-dump --split-files "SRR8311164"
gz1="$(_compress_if_exists 'SRR8311164_1' || true)"
gz2="$(_compress_if_exists 'SRR8311164_2' || true)"
gzs="$(_compress_if_exists 'SRR8311164' || true)"

fasterq-dump --split-files "SRR8311165"
gz1="$(_compress_if_exists 'SRR8311165_1' || true)"
gz2="$(_compress_if_exists 'SRR8311165_2' || true)"
gzs="$(_compress_if_exists 'SRR8311165' || true)"

fasterq-dump --split-files "SRR8311166"
gz1="$(_compress_if_exists 'SRR8311166_1' || true)"
gz2="$(_compress_if_exists 'SRR8311166_2' || true)"
gzs="$(_compress_if_exists 'SRR8311166' || true)"

fasterq-dump --split-files "SRR8311167"
gz1="$(_compress_if_exists 'SRR8311167_1' || true)"
gz2="$(_compress_if_exists 'SRR8311167_2' || true)"
gzs="$(_compress_if_exists 'SRR8311167' || true)"

fasterq-dump --split-files "SRR8311168"
gz1="$(_compress_if_exists 'SRR8311168_1' || true)"
gz2="$(_compress_if_exists 'SRR8311168_2' || true)"
gzs="$(_compress_if_exists 'SRR8311168' || true)"

fasterq-dump --split-files "SRR8311169"
gz1="$(_compress_if_exists 'SRR8311169_1' || true)"
gz2="$(_compress_if_exists 'SRR8311169_2' || true)"
gzs="$(_compress_if_exists 'SRR8311169' || true)"

fasterq-dump --split-files "SRR8311170"
gz1="$(_compress_if_exists 'SRR8311170_1' || true)"
gz2="$(_compress_if_exists 'SRR8311170_2' || true)"
gzs="$(_compress_if_exists 'SRR8311170' || true)"

fasterq-dump --split-files "SRR8311171"
gz1="$(_compress_if_exists 'SRR8311171_1' || true)"
gz2="$(_compress_if_exists 'SRR8311171_2' || true)"
gzs="$(_compress_if_exists 'SRR8311171' || true)"

fasterq-dump --split-files "SRR8311172"
gz1="$(_compress_if_exists 'SRR8311172_1' || true)"
gz2="$(_compress_if_exists 'SRR8311172_2' || true)"
gzs="$(_compress_if_exists 'SRR8311172' || true)"

fasterq-dump --split-files "SRR8311173"
gz1="$(_compress_if_exists 'SRR8311173_1' || true)"
gz2="$(_compress_if_exists 'SRR8311173_2' || true)"
gzs="$(_compress_if_exists 'SRR8311173' || true)"

fasterq-dump --split-files "SRR8311174"
gz1="$(_compress_if_exists 'SRR8311174_1' || true)"
gz2="$(_compress_if_exists 'SRR8311174_2' || true)"
gzs="$(_compress_if_exists 'SRR8311174' || true)"

fasterq-dump --split-files "SRR8311175"
gz1="$(_compress_if_exists 'SRR8311175_1' || true)"
gz2="$(_compress_if_exists 'SRR8311175_2' || true)"
gzs="$(_compress_if_exists 'SRR8311175' || true)"

fasterq-dump --split-files "SRR8311176"
gz1="$(_compress_if_exists 'SRR8311176_1' || true)"
gz2="$(_compress_if_exists 'SRR8311176_2' || true)"
gzs="$(_compress_if_exists 'SRR8311176' || true)"

fasterq-dump --split-files "SRR8311177"
gz1="$(_compress_if_exists 'SRR8311177_1' || true)"
gz2="$(_compress_if_exists 'SRR8311177_2' || true)"
gzs="$(_compress_if_exists 'SRR8311177' || true)"

fasterq-dump --split-files "SRR8311178"
gz1="$(_compress_if_exists 'SRR8311178_1' || true)"
gz2="$(_compress_if_exists 'SRR8311178_2' || true)"
gzs="$(_compress_if_exists 'SRR8311178' || true)"

fasterq-dump --split-files "SRR8311179"
gz1="$(_compress_if_exists 'SRR8311179_1' || true)"
gz2="$(_compress_if_exists 'SRR8311179_2' || true)"
gzs="$(_compress_if_exists 'SRR8311179' || true)"

fasterq-dump --split-files "SRR8311180"
gz1="$(_compress_if_exists 'SRR8311180_1' || true)"
gz2="$(_compress_if_exists 'SRR8311180_2' || true)"
gzs="$(_compress_if_exists 'SRR8311180' || true)"

fasterq-dump --split-files "SRR8311181"
gz1="$(_compress_if_exists 'SRR8311181_1' || true)"
gz2="$(_compress_if_exists 'SRR8311181_2' || true)"
gzs="$(_compress_if_exists 'SRR8311181' || true)"

fasterq-dump --split-files "SRR8311182"
gz1="$(_compress_if_exists 'SRR8311182_1' || true)"
gz2="$(_compress_if_exists 'SRR8311182_2' || true)"
gzs="$(_compress_if_exists 'SRR8311182' || true)"

fasterq-dump --split-files "SRR8311183"
gz1="$(_compress_if_exists 'SRR8311183_1' || true)"
gz2="$(_compress_if_exists 'SRR8311183_2' || true)"
gzs="$(_compress_if_exists 'SRR8311183' || true)"

fasterq-dump --split-files "SRR8311184"
gz1="$(_compress_if_exists 'SRR8311184_1' || true)"
gz2="$(_compress_if_exists 'SRR8311184_2' || true)"
gzs="$(_compress_if_exists 'SRR8311184' || true)"


# Option B: Direct download (larger .sra files)
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967339/SRR16967339"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967340/SRR16967340"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967341/SRR16967341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967342/SRR16967342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967343/SRR16967343"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967344/SRR16967344"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967345/SRR16967345"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967346/SRR16967346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967347/SRR16967347"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967348/SRR16967348"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311135/SRR8311135"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311136/SRR8311136"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311137/SRR8311137"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311138/SRR8311138"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311139/SRR8311139"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311140/SRR8311140"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311141/SRR8311141"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311142/SRR8311142"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311143/SRR8311143"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311144/SRR8311144"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311145/SRR8311145"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311146/SRR8311146"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311147/SRR8311147"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311148/SRR8311148"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311149/SRR8311149"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311150/SRR8311150"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311151/SRR8311151"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311152/SRR8311152"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311153/SRR8311153"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311154/SRR8311154"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311155/SRR8311155"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311156/SRR8311156"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311157/SRR8311157"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311158/SRR8311158"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311159/SRR8311159"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311160/SRR8311160"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311161/SRR8311161"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311162/SRR8311162"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311163/SRR8311163"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311164/SRR8311164"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311165/SRR8311165"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311166/SRR8311166"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311167/SRR8311167"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311168/SRR8311168"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311169/SRR8311169"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311170/SRR8311170"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311171/SRR8311171"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311172/SRR8311172"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311173/SRR8311173"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311174/SRR8311174"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311175/SRR8311175"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311176/SRR8311176"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311177/SRR8311177"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311178/SRR8311178"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311179/SRR8311179"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311180/SRR8311180"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311181/SRR8311181"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311182/SRR8311182"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311183/SRR8311183"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311184/SRR8311184"

# --- Additional data files ---
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967345/SRR16967345"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967347/SRR16967347"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967340/SRR16967340"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967342/SRR16967342"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967344/SRR16967344"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967346/SRR16967346"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967348/SRR16967348"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311135/SRR8311135"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311136/SRR8311136"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311137/SRR8311137"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311138/SRR8311138"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311139/SRR8311139"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311140/SRR8311140"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311141/SRR8311141"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311142/SRR8311142"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311143/SRR8311143"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311144/SRR8311144"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311145/SRR8311145"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311146/SRR8311146"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311147/SRR8311147"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311148/SRR8311148"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311149/SRR8311149"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311150/SRR8311150"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311151/SRR8311151"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311152/SRR8311152"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311153/SRR8311153"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311154/SRR8311154"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311155/SRR8311155"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311156/SRR8311156"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311157/SRR8311157"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311158/SRR8311158"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311159/SRR8311159"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311160/SRR8311160"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311161/SRR8311161"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311162/SRR8311162"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311163/SRR8311163"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311164/SRR8311164"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311165/SRR8311165"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311166/SRR8311166"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311167/SRR8311167"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311168/SRR8311168"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311169/SRR8311169"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311170/SRR8311170"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311171/SRR8311171"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311172/SRR8311172"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311173/SRR8311173"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311174/SRR8311174"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311175/SRR8311175"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311176/SRR8311176"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311177/SRR8311177"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311178/SRR8311178"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311179/SRR8311179"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311180/SRR8311180"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967339/SRR16967339"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967341/SRR16967341"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16967343/SRR16967343"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311181/SRR8311181"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311182/SRR8311182"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311183/SRR8311183"
curl -L -O -C - "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8311184/SRR8311184"

echo "Download complete. Files saved to $OUTDIR"