The {assembly_info['assembly.name']} assembly was submitted by {assembly_info['assembly.submitter']} " + f"and last updated on {assembly_info['assembly.date']}. The assembly is on the {assembly_info['assembly.level']} " + f"level, consisting of {assembly_info['contig.count']} contigs assembled into {assembly_info['scaffold.count']} scaffolds. " + f"The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. " + f"The N50 length for the contigs is {assembly_info['contig.n50']} while the scaffold N50 is {assembly_info['scaffold.n50']}.
", + file=assembly_out + ) + + with open(output_dir / f"{production_name}_annotation.html", "w") as annotation_out: + print( + "Genome annotation was generated using the " + "Ensembl vertebrate annotation pipeline. " + "
In accordance with the " + "Fort Lauderdale Agreement, please check the publication " + "status of the genome/assembly before publishing any genome-wide analyses using these data.
", + file=annotation_out + ) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Prepare static content files for main release") + parser.add_argument("-o", "--output_dir", type=str, help="Output directory for files. Uses current dir by default.") + parser.add_argument("-d", "--db_name", help="Database name", required=True) + parser.add_argument("-s", "--host", help="Host server", required=True) + parser.add_argument("-p", "--port", type=int, help="Host server port", required=True) + + args = parser.parse_args() + + server_info = { + "server": { + "db_host": args.host, + "db_port": args.port, + "db_user": "ensro", + }, + } + + db = args.db_name + output_dir = Path(args.output_dir) + output_dir.mkdir(parents=True, exist_ok=True) + + # Fetch assembly accession and production name from the core database + core_query = ( + "SELECT meta_key, meta_value FROM meta WHERE meta_key IN " + "('assembly.accession', 'species.production_name');" + ) + core_meta = mysql_fetch_data( + core_query, + host=server_info["server"]["db_host"], + user=server_info["server"]["db_user"], + port=server_info["server"]["db_port"], + database=db, + ) + + core_dict = {meta_pair[0]: meta_pair[1] for meta_pair in core_meta} + upper_production_name = core_dict['species.production_name'].capitalize() + + # Get assembly info and write content files + assembly_info = get_assembly_info(core_dict['assembly.accession']) + write_content(assembly_info, output_dir, upper_production_name) diff --git a/src/python/ensembl/genes/content/main_static_murine_content.py b/src/python/ensembl/genes/content/main_static_murine_content.py new file mode 100644 index 0000000..461af2b --- /dev/null +++ b/src/python/ensembl/genes/content/main_static_murine_content.py @@ -0,0 +1,150 @@ +import argparse +import pymysql +import requests +import xmltodict +from pathlib import Path + + +def mysql_fetch_data(query, database, host, port, user): + """ + Fetch data from a MySQL database based on a provided query. + + Args: + query (str): SQL query to execute. + database (str): Database name to connect to. + host (str): Host address of the MySQL server. + port (int): Port number of the MySQL server. + user (str): Username for the MySQL server. + + Returns: + tuple: A tuple containing the fetched data. + """ + try: + conn = pymysql.connect(host=host, user=user, port=port, database=database.strip()) + cursor = conn.cursor() + cursor.execute(query) + info = cursor.fetchall() + except pymysql.Error as err: + print(f"Database error: {err}") + info = None + finally: + cursor.close() + conn.close() + return info + + +def get_assembly_info(accession): + """ + Retrieve assembly information from the ENA API for a given accession. + + Args: + accession (str): The assembly accession number to fetch information for. + + Returns: + dict: A dictionary containing assembly attributes such as name, level, submitter, and counts. + """ + assembly_url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}" + assembly_xml = requests.get(assembly_url) + assembly_dict = xmltodict.parse(assembly_xml.text) + assembly_attribs = assembly_dict["ASSEMBLY_SET"]["ASSEMBLY"]["ASSEMBLY_ATTRIBUTES"]["ASSEMBLY_ATTRIBUTE"] + + return_dict = {} + + # Retrieve specific attributes with error handling + return_dict["assembly.name"] = assembly_dict["ASSEMBLY_SET"]["ASSEMBLY"].get("NAME", "") + return_dict["assembly.level"] = assembly_dict["ASSEMBLY_SET"]["ASSEMBLY"].get("ASSEMBLY_LEVEL", "") + return_dict["assembly.submitter"] = assembly_dict["ASSEMBLY_SET"]["ASSEMBLY"]["IDENTIFIERS"]["SUBMITTER_ID"].get("@namespace", "") + + # Fetch specific attributes based on tags + for attrib_set in assembly_attribs: + if attrib_set["TAG"] == "count-contig": + return_dict["contig.count"] = attrib_set["VALUE"] + elif attrib_set["TAG"] == "scaffold-count": + return_dict["scaffold.count"] = attrib_set["VALUE"] + elif attrib_set["TAG"] == "ENA-LAST-UPDATED": + return_dict["assembly.date"] = attrib_set["VALUE"] + elif attrib_set["TAG"] == "n50": + return_dict["scaffold.n50"] = attrib_set["VALUE"] + elif attrib_set["TAG"] == "contig-n50": + return_dict["contig.n50"] = attrib_set["VALUE"] + + return return_dict + + +def write_content(assembly_info, output_dir, production_name, strain): + """ + Write assembly and annotation content to HTML files. + + Args: + assembly_info (dict): Assembly information to be written. + output_dir (Path): Directory path for output files. + production_name (str): Name used to title the output files. + """ + with open(output_dir / f"{production_name}_assembly.html", "w") as assembly_out: + print( + f"The assembly for {strain} was generated as part of The Mouse Genomes Project " + f"[https://www.mousegenomes.org/], additional strains can be found in Ensembl " + f"[https://www.ensembl.org/Mus_musculus/Info/Strains].
" + f"The assembly is on the {assembly_info['assembly.level']} " + f"level, consisting of {assembly_info['contig.count']} contigs assembled into {assembly_info['scaffold.count']} scaffolds. " + f"The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. " + f"The N50 length for the contigs is {assembly_info['contig.n50']} while the scaffold N50 is {assembly_info['scaffold.n50']}.
", + file=assembly_out + ) + + with open(output_dir / f"{production_name}_annotation.html", "w") as annotation_out: + print( + f"Genome annotation was generated by mapping GENCODE M30 [https://www.gencodegenes.org/mouse/release_M30.html] " + f"genes and transcripts via the Ensembl Human automated annotation system " + f"[https://beta.ensembl.org/help/articles/human-genome-automated-annotation], supplemented by methods from the " + f"Ensembl vertebrate annotation pipeline [https://beta.ensembl.org/help/articles/vertebrate-genome-annotation]. " + f"Mapped GENCODE structures served as the primary evidence with gaps in the annotations filled using aligned short-read " + f"transcriptomic data and full-length transcripts derived from PacBio IsoSeq long-read data." + f"
In accordance with the " + f"Fort Lauderdale Agreement, please check the publication " + f"status of the genome/assembly before publishing any genome-wide analyses using these data.
", + file=annotation_out + ) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Prepare static content files for main release") + parser.add_argument("-o", "--output_dir", type=str, help="Output directory for files. Uses current dir by default.") + parser.add_argument("-d", "--db_name", help="Database name", required=True) + parser.add_argument("-s", "--host", help="Host server", required=True) + parser.add_argument("-p", "--port", type=int, help="Host server port", required=True) + + args = parser.parse_args() + + server_info = { + "server": { + "db_host": args.host, + "db_port": args.port, + "db_user": "ensro", + }, + } + + db = args.db_name + output_dir = Path(args.output_dir) + output_dir.mkdir(parents=True, exist_ok=True) + + # Fetch assembly accession and production name from the core database + core_query = ( + "SELECT meta_key, meta_value FROM meta WHERE meta_key IN " + "('assembly.accession', 'species.production_name', 'species.strain');" + ) + core_meta = mysql_fetch_data( + core_query, + host=server_info["server"]["db_host"], + user=server_info["server"]["db_user"], + port=server_info["server"]["db_port"], + database=db, + ) + + core_dict = {meta_pair[0]: meta_pair[1] for meta_pair in core_meta} + upper_production_name = core_dict['species.production_name'].capitalize() + + # Get assembly info and write content files + assembly_info = get_assembly_info(core_dict['assembly.accession']) + strain = core_dict['species.strain'] + write_content(assembly_info, output_dir, upper_production_name, strain)