{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b9c59e0e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import re\n",
    "from pathlib import Path\n",
    "\n",
    "# ============================================================\n",
    "# Input / output\n",
    "# ============================================================\n",
    "\n",
    "GTF_FILE = Path(\n",
    "    \"/s/chromatin/m/nobackup/ahmed/GitRepositries/\"\n",
    "    \"DeepPlant/data/arabidopsis/gtf/Arabidopsis.gtf\"\n",
    ")\n",
    "\n",
    "OUTPUT_DIR = GTF_FILE.parent\n",
    "\n",
    "CODING_FILE = OUTPUT_DIR / \"coding_genes.txt\"\n",
    "NONCODING_FILE = OUTPUT_DIR / \"noncoding_genes.txt\"\n",
    "NONTRANSLATING_FILE = OUTPUT_DIR / \"nontranslating_CDS_genes.txt\"\n",
    "\n",
    "\n",
    "# ============================================================\n",
    "# Biotype definitions\n",
    "# ============================================================\n",
    "\n",
    "NONCODING_BIOTYPES = {\n",
    "    \"lncRNA\",\n",
    "    \"miRNA\",\n",
    "    \"ncRNA\",\n",
    "    \"rRNA\",\n",
    "    \"snRNA\",\n",
    "    \"snoRNA\",\n",
    "    \"tRNA\",\n",
    "}\n",
    "\n",
    "PROTEIN_CODING_BIOTYPE = \"protein_coding\"\n",
    "\n",
    "SPECIAL_BIOTYPE = \"nontranslating_CDS\"\n",
    "\n",
    "\n",
    "# ============================================================\n",
    "# Parse GTF attributes\n",
    "# ============================================================\n",
    "\n",
    "def parse_attributes(attribute_string):\n",
    "    \"\"\"\n",
    "    Parse the attributes field of a GTF line.\n",
    "\n",
    "    Example:\n",
    "        gene_id \"AT1G01010\";\n",
    "        gene_biotype \"protein_coding\";\n",
    "    \"\"\"\n",
    "\n",
    "    attributes = {}\n",
    "\n",
    "    for match in re.finditer(r'(\\S+)\\s+\"([^\"]*)\"', attribute_string):\n",
    "        key, value = match.groups()\n",
    "        attributes[key] = value\n",
    "\n",
    "    return attributes\n",
    "\n",
    "\n",
    "# ============================================================\n",
    "# Main\n",
    "# ============================================================\n",
    "\n",
    "def main():\n",
    "\n",
    "    if not GTF_FILE.exists():\n",
    "        raise FileNotFoundError(\n",
    "            f\"GTF file not found:\\n{GTF_FILE}\"\n",
    "        )\n",
    "\n",
    "    coding_genes = set()\n",
    "    noncoding_genes = set()\n",
    "    nontranslating_genes = set()\n",
    "\n",
    "    biotype_counts = {}\n",
    "    mitochondrial_or_chloroplast_genes = set()\n",
    "\n",
    "    with open(GTF_FILE, \"r\") as f:\n",
    "\n",
    "        for line_number, line in enumerate(f, start=1):\n",
    "\n",
    "            line = line.strip()\n",
    "\n",
    "            if not line or line.startswith(\"#\"):\n",
    "                continue\n",
    "\n",
    "            fields = line.split(\"\\t\")\n",
    "\n",
    "            if len(fields) != 9:\n",
    "                print(\n",
    "                    f\"Warning: skipping malformed line {line_number}\"\n",
    "                )\n",
    "                continue\n",
    "\n",
    "            feature = fields[2]\n",
    "            attributes_string = fields[8]\n",
    "\n",
    "            # We only need gene-level annotations\n",
    "            if feature != \"gene\":\n",
    "                continue\n",
    "\n",
    "            attributes = parse_attributes(attributes_string)\n",
    "\n",
    "            gene_id = attributes.get(\"gene_id\")\n",
    "\n",
    "            if gene_id is None:\n",
    "                print(\n",
    "                    f\"Warning: no gene_id found on line {line_number}\"\n",
    "                )\n",
    "                continue\n",
    "\n",
    "            # Remove version suffix if present\n",
    "            # Example: AT1G01010.1 -> AT1G01010\n",
    "            gene_id = gene_id.split(\".\")[0]\n",
    "\n",
    "            # =================================================\n",
    "            # Remove mitochondrial genes\n",
    "            # =================================================\n",
    "\n",
    "            if gene_id.upper().startswith((\"ATMG\", \"ATCG\")):\n",
    "                mitochondrial_or_chloroplast_genes.add(gene_id)\n",
    "                continue\n",
    "\n",
    "            # =================================================\n",
    "            # Get gene biotype\n",
    "            # =================================================\n",
    "\n",
    "            biotype = (\n",
    "                attributes.get(\"gene_biotype\")\n",
    "                or attributes.get(\"gene_type\")\n",
    "                or attributes.get(\"biotype\")\n",
    "                or \"unknown\"\n",
    "            )\n",
    "\n",
    "            biotype_counts[biotype] = (\n",
    "                biotype_counts.get(biotype, 0) + 1\n",
    "            )\n",
    "\n",
    "            # =================================================\n",
    "            # Classify gene\n",
    "            # =================================================\n",
    "\n",
    "            if biotype == PROTEIN_CODING_BIOTYPE:\n",
    "\n",
    "                coding_genes.add(gene_id)\n",
    "\n",
    "            elif biotype in NONCODING_BIOTYPES:\n",
    "\n",
    "                noncoding_genes.add(gene_id)\n",
    "\n",
    "            elif biotype == SPECIAL_BIOTYPE:\n",
    "\n",
    "                nontranslating_genes.add(gene_id)\n",
    "\n",
    "    # =========================================================\n",
    "    # Sort\n",
    "    # =========================================================\n",
    "\n",
    "    coding_genes = sorted(coding_genes)\n",
    "    noncoding_genes = sorted(noncoding_genes)\n",
    "    nontranslating_genes = sorted(nontranslating_genes)\n",
    "    mitochondrial_or_chloroplast_genes = sorted(mitochondrial_or_chloroplast_genes)\n",
    "\n",
    "    # =========================================================\n",
    "    # Write output files\n",
    "    # =========================================================\n",
    "\n",
    "    with open(CODING_FILE, \"w\") as f:\n",
    "        for gene_id in coding_genes:\n",
    "            f.write(gene_id + \"\\n\")\n",
    "\n",
    "    with open(NONCODING_FILE, \"w\") as f:\n",
    "        for gene_id in noncoding_genes:\n",
    "            f.write(gene_id + \"\\n\")\n",
    "\n",
    "    with open(NONTRANSLATING_FILE, \"w\") as f:\n",
    "        for gene_id in nontranslating_genes:\n",
    "            f.write(gene_id + \"\\n\")\n",
    "\n",
    "    # =========================================================\n",
    "    # Summary\n",
    "    # =========================================================\n",
    "\n",
    "    print(\"\\n========================================\")\n",
    "    print(\"Arabidopsis gene classification\")\n",
    "    print(\"========================================\")\n",
    "\n",
    "    print(f\"\\nProtein-coding genes : {len(coding_genes):,}\")\n",
    "    print(f\"Non-coding genes     : {len(noncoding_genes):,}\")\n",
    "    print(f\"Nontranslating CDS   : {len(nontranslating_genes):,}\")\n",
    "    print(f\"Mitochondrial or Chloroplast genes  : {len(mitochondrial_or_chloroplast_genes):,}\")\n",
    "\n",
    "    print(\"\\nBiotypes retained:\")\n",
    "    for biotype, count in sorted(biotype_counts.items()):\n",
    "        print(f\"  {biotype:25s} {count:,}\")\n",
    "\n",
    "    print(\"\\nOutput files:\")\n",
    "    print(f\"  Coding       : {CODING_FILE}\")\n",
    "    print(f\"  Non-coding   : {NONCODING_FILE}\")\n",
    "    print(f\"  Nontranslating: {NONTRANSLATING_FILE}\")\n",
    "\n",
    "    print(\"\\nFirst mitochondrial genes removed:\")\n",
    "    for gene_id in mitochondrial_or_chloroplast_genes[:10]:\n",
    "        print(f\"  {gene_id}\")\n",
    "\n",
    "    if len(mitochondrial_or_chloroplast_genes) > 10:\n",
    "        print(f\"  ... and {len(mitochondrial_or_chloroplast_genes) - 10:,} more\")\n",
    "\n",
    "\n",
    "if __name__ == \"__main__\":\n",
    "    main()"
   ]
  }
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