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"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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"language_info": {
"name": "python"
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