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.gitattributes

@@ -62,3 +62,4 @@ predictions_truth/all_models_predictions_long.csv filter=lfs diff=lfs merge=lfs
 Supp1.csv filter=lfs diff=lfs merge=lfs -text
 Supp2.xlsx filter=lfs diff=lfs merge=lfs -text
 tRNA_intership.html filter=lfs diff=lfs merge=lfs -text
+ftp_urls.txt filter=lfs diff=lfs merge=lfs -text

ftp_urls.txt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e77a3ce4a9b53f07f62088c0a0e1afdcacda0f66f4085184f2bb33cae5478c36
+size 32160334

full.sh

@@ -0,0 +1,254 @@
+#!/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"
+