full.sh

#!/usr/bin/env bash
set -euo pipefail
IFS=$'\n\t'

# ==========================================================
#  ARAGORN pipeline for genomes listed in ftp_urls.txt
#  Adds: GC content + normalized 4-mers + TypePerAcc to NDJSON
#  Keeps original file operations and structure
# ==========================================================

# --- Configuration ---
THREADS=16
FTP_LIST="ftp_urls.txt"
GENOMES_DIR="genomes"
OUTDIR="aragorn_out"
LOGDIR="logs"
TMPDIR_BASE="tmp_aragorn"
LINES_DIR="json_lines"          # per-genome NDJSON lines (new)
AGG_JSON="FEATURES_ALL.ndjson"  # merged NDJSON (new)

# --- Setup ---
mkdir -p "$GENOMES_DIR" "$OUTDIR" "$LOGDIR" "$TMPDIR_BASE" "$LINES_DIR"
: > "$AGG_JSON"

# --- Helpers: feature calculators ---

# 1) GC content
gc_content() {
  local fasta="$1"
  awk '
    BEGIN{A=0;C=0;G=0;T=0}
    /^>/ {next}
    {
      for(i=1;i<=length($0);i++){
        b=toupper(substr($0,i,1))
        if(b=="U") b="T"
        if(b=="A") A++
        else if(b=="C") C++
        else if(b=="G") G++
        else if(b=="T") T++
      }
    }
    END{
      total=A+C+G+T
      gc=(total>0)?(G+C)/total:0
      printf("gc_fraction\t%.6f\n", gc)
      printf("gc_percent\t%.3f\n", gc*100)
      printf("length_acgt\t%d\n", total)
      printf("count_A\t%d\ncount_C\t%d\ncount_G\t%d\ncount_T\t%d\n", A,C,G,T)
    }' "$fasta"
}

# 2) Normalized 4-mers (256 combos), freq = count / sum(L_i-3)
tetra_norm() {
  local fasta="$1"
  awk '
    function count_seq(seq){
      n=length(seq)
      if(n<4) return
      for(i=1;i<=n-3;i++){
        k=substr(seq,i,4)
        if(k ~ /^[ACGT]{4}$/) cnt[k]++
      }
      win_total += (n-3)
    }
    BEGIN{
      split("A C G T", B, " ")
      for(i1=1;i1<=4;i1++)
        for(i2=1;i2<=4;i2++)
          for(i3=1;i3<=4;i3++)
            for(i4=1;i4<=4;i4++){
              k=B[i1] B[i2] B[i3] B[i4]
              cnt[k]=0
            }
      win_total=0
    }
    /^>/{
      if(seq!=""){ count_seq(seq) }
      seq=""
      next
    }
    {
      s=toupper($0)
      gsub(/U/,"T",s)
      gsub(/[^ACGT]/,"N",s)
      seq=seq s
    }
    END{
      if(seq!=""){ count_seq(seq) }
      denom = (win_total>0)?win_total:1
      split("A C G T", B, " ")
      for(i1=1;i1<=4;i1++)
        for(i2=1;i2<=4;i2++)
          for(i3=1;i3<=4;i3++)
            for(i4=1;i4<=4;i4++){
              k=B[i1] B[i2] B[i3] B[i4]
              freq = cnt[k]/denom
              printf("%s\t%.8f\n", k, freq)
            }
      printf("windows_total\t%d\n", win_total)
    }' "$fasta"
}

# 3) Type Per Acc from ARAGORN output (like your example)
trna_type_per_acc() {
  local aragorn_txt="$1" acc="$2"
  awk -v ACC="$acc" '
    BEGIN{ IGNORECASE=1 }
    {
      line=$0
      if(line ~ /tRNA/){
        aa=""
        if(match(line, /tRNA-([A-Za-z]+)/, m)){ aa=m[1] }
        else if(match(line, /^[[:space:]]*([A-Za-z]{3})[[:space:]]*\(/, m)){ aa=m[1] }
        ac=""
        if(match(line, /\(([A-Za-z]{3})\)/, n)){ ac=n[1] }
        if(ac!=""){
          gsub(/u/,"T",ac); gsub(/U/,"T",ac); ac=toupper(ac); gsub(/[^ACGT]/,"N",ac)
        }
        if(aa!=""){ aa=tolower(aa); aa=toupper(substr(aa,1,1)) substr(aa,2,2) }
        if(aa!="" && ac!=""){
          key = ACC "_genome_" aa "_" ac
          counts[key]++
        }
      }
    }
    END{ for(k in counts) printf("%d %s\n", counts[k], k) }
  ' "$aragorn_txt" | sort -k1,1nr -k2,2
}

# 4) Build one NDJSON line into json_lines/<ACC>.ndjson
emit_ndjson_line() {
  local acc="$1" gc_fp="$2" tetra_fp="$3" tpa_fp="$4" out_line_fp="$5"
  {
    printf '{'
    printf '"acc":"%s",' "$acc"

    printf '"gc":{'
    awk '
      $1=="gc_fraction"{printf("\"fraction\":%s", $2); next}
      $1=="gc_percent"{printf(",\"percent\":%s", $2); next}
      $1=="length_acgt"{printf(",\"length\":%s", $2); next}
      $1=="count_A"{printf(",\"A\":%s", $2); next}
      $1=="count_C"{printf(",\"C\":%s", $2); next}
      $1=="count_G"{printf(",\"G\":%s", $2); next}
      $1=="count_T"{printf(",\"T\":%s", $2); next}
    ' "$gc_fp"
    printf '},'

    printf '"tetra_norm":{'
    awk '
      BEGIN{first=1}
      {
        if($1=="windows_total"){ wt=$2; next }
        if(!first) printf(",")
        printf("\"%s\":%s", $1, $2)
        first=0
      }
      END{
        if(!first) printf(",")
        printf("\"windows_total\":%s", (wt ? wt : 0))
      }
    ' "$tetra_fp"
    printf '},'

    printf '"trna_type_per_acc":['
    if [ -s "$tpa_fp" ]; then
      awk '
        BEGIN{first=1}
        {
          if(!first) printf(",")
          printf("{\"count\":%d,\"label\":\"%s\"}", $1, $2)
          first=0
        }' "$tpa_fp"
    fi
    printf ']'

    printf '}\n'
  } > "$out_line_fp"
}

# --- Function for processing one genome (kept as in your script, extended) ---
process_one() {
    url="$1"
    acc=$(basename "$url" | sed 's/_genomic.*//')
    tmpdir="$TMPDIR_BASE/${acc}_tmp"
    mkdir -p "$tmpdir"
    cd "$tmpdir" || exit 1

    echo "[INFO] Processing $acc" >&2

    # Download genome
    wget -q -O "${acc}.fna.gz" "$url"
    if [ ! -s "${acc}.fna.gz" ]; then
        echo "[ERROR] Failed to download $acc" >&2
        rm -rf "$tmpdir"
        return
    fi

    # Unpack
    gunzip -f "${acc}.fna.gz"
    fasta=$(ls *.fna *.fa *.fasta 2>/dev/null | head -n 1)
    if [ ! -f "$fasta" ]; then
        echo "[ERROR] No FASTA found for $acc after extraction" >&2
        rm -rf "$tmpdir"
        return
    fi

    # Run ARAGORN (unchanged)
    out_file="../../$OUTDIR/${acc}.txt"
    log_file="../../$LOGDIR/${acc}.log"

    echo "[RUN] ARAGORN on $acc" >&2
    aragorn -t -l -gc1 -w -o "$out_file" "$fasta" >"$log_file" 2>&1

    if [ -s "$out_file" ]; then
        echo "[OK] $acc done" >&2
    else
        echo "[FAIL] ARAGORN empty output for $acc" >&2
        echo "$acc" >> "../../$LOGDIR/failed_genomes.txt"
        : > "$out_file"   # keep an empty file to be parsable
    fi

    # --- NEW: compute features and emit NDJSON line (all stays in tmpdir / json_lines) ---
    gc_fp="${acc}.gc.tsv"
    tetra_fp="${acc}.tetra.tsv"
    tpa_fp="${acc}.tpa.txt"

    gc_content "$fasta" > "$gc_fp"
    tetra_norm  "$fasta" > "$tetra_fp"
    trna_type_per_acc "$out_file" "$acc" > "$tpa_fp" || true

    # write single-line NDJSON per genome
    json_line="../../$LINES_DIR/${acc}.ndjson"
    emit_ndjson_line "$acc" "$gc_fp" "$tetra_fp" "$tpa_fp" "$json_line"

    # Cleanup tmp (unchanged)
    cd - >/dev/null
    rm -rf "$tmpdir"
}

export -f process_one gc_content tetra_norm trna_type_per_acc emit_ndjson_line
export OUTDIR LOGDIR TMPDIR_BASE LINES_DIR

# --- Parallel execution (unchanged) ---
echo "[PIPELINE] Starting with $(wc -l < "$FTP_LIST") genomes using $THREADS threads..."
cat "$FTP_LIST" | parallel -j "$THREADS" process_one {}

# --- Merge NDJSON lines to a single file (new, simple, sequential) ---
# deterministic order by filename
ls "$LINES_DIR"/*.ndjson 2>/dev/null | sort | xargs cat -- > "$AGG_JSON" || true

echo "[PIPELINE] All done. NDJSON -> $AGG_JSON"