update_description

ensembl.io.genomio.annotation.update_description

Update descriptions from a functional annotation file into a core database.

FEAT_TABLE = {'gene': 'gene', 'mobile_element': 'gene', 'transcript': 'transcript'} module-attribute

FeatStruct = Tuple[str, str, str] module-attribute

get_core_data(session, table, match_xrefs=False)

Returns the table descriptions from a core database.

Parameters:

Name	Type	Description	Default
session	Session	Session open on a core database.	required
table	str	"gene" or "transcript" table from the core database.	required
match_xrefs	bool	If the IDs do not match, try to match an Xref ID instead.	False

Source code in src/python/ensembl/io/genomio/annotation/update_description.py

def get_core_data(session: Session, table: str, match_xrefs: bool = False) -> Dict[str, FeatStruct]:
    """Returns the table descriptions from a core database.

    Args:
        session: Session open on a core database.
        table: "gene" or "transcript" table from the core database.
        match_xrefs: If the IDs do not match, try to match an Xref ID instead.
    """

    if table == "gene":
        stmt = (
            select(Gene.gene_id, Gene.stable_id, Gene.description, Xref.dbprimary_acc)
            .select_from(Gene)
            .outerjoin(
                ObjectXref,
                and_(Gene.gene_id == ObjectXref.ensembl_id, ObjectXref.ensembl_object_type == "gene"),
            )
            .outerjoin(Xref)
        )
    elif table == "transcript":
        stmt = (
            select(Transcript.transcript_id, Transcript.stable_id, Transcript.description, Xref.dbprimary_acc)
            .select_from(Transcript)
            .outerjoin(
                ObjectXref,
                and_(
                    Transcript.transcript_id == ObjectXref.ensembl_id,
                    ObjectXref.ensembl_object_type == "transcript",
                ),
            )
            .outerjoin(Xref)
        )
    else:
        raise ValueError(f"Table {table} is not supported")

    feat_data = {}
    for row in session.execute(stmt):
        (feat_id, stable_id, desc, xref_name) = row
        feat_struct: FeatStruct = (feat_id, stable_id, desc)
        feat_data[stable_id.lower()] = feat_struct
        if match_xrefs and xref_name:
            feat_data[xref_name.lower()] = feat_struct

    return feat_data

load_descriptions(session, func_file, report=False, do_update=False, match_xrefs=True)

Loads gene and transcript descriptions into a core database.

Parameters:

Name	Type	Description	Default
session	Session	Session open on a core database.	required
func_file	Path	JSON file with the annotation information.	required
report	bool	Print the mapping of changes to perform in the standard output.	False
do_update	bool	Actually update the core database.	False
match_xrefs	bool	If the IDs do not match, try to match an Xref ID instead.	True

Source code in src/python/ensembl/io/genomio/annotation/update_description.py

def load_descriptions(
    session: Session,
    func_file: Path,
    report: bool = False,
    do_update: bool = False,
    match_xrefs: bool = True,
) -> None:
    """Loads gene and transcript descriptions into a core database.

    Args:
        session: Session open on a core database.
        func_file: JSON file with the annotation information.
        report: Print the mapping of changes to perform in the standard output.
        do_update: Actually update the core database.
        match_xrefs: If the IDs do not match, try to match an Xref ID instead.
    """
    func = get_json(func_file)
    logging.info(f"{len(func)} annotations from {func_file}")
    table_to_update = {"gene": Gene, "transcript": Transcript}
    for table, mapped_table in table_to_update.items():
        logging.info(f"Checking {table} descriptions")
        feat_func = [feat for feat in func if feat["object_type"] == table]
        logging.info(f"{len(feat_func)} {table} annotations from {func_file}")
        feat_data = get_core_data(session, table, match_xrefs)
        logging.info(f"Loaded {len(feat_data)} {table} data")

        stats = {
            "not_supported": 0,
            "not_found": 0,
            "same": 0,
            "same_empty": 0,
            "empty_but_xref": 0,
            "to_update_replace": 0,
            "to_update_remove": 0,
        }
        # Compare, only keep the descriptions that have changed
        features_to_update = _get_features_to_update(
            table, feat_func, feat_data, stats, report=report, do_update=do_update, match_xrefs=match_xrefs
        )

        # Show stats for this feature type
        for stat, count in stats.items():
            if count == 0:
                continue
            logging.info(f"{stat} = {count}")

        if do_update:
            logging.info(f"Now updating {len(features_to_update)} rows...")
            session.bulk_update_mappings(mapped_table, features_to_update)
            session.commit()

main()

Main script entry-point.

Source code in src/python/ensembl/io/genomio/annotation/update_description.py

def main() -> None:
    """Main script entry-point."""
    parser = ArgumentParser(description=__doc__)
    parser.add_server_arguments(include_database=True)
    parser.add_argument_src_path("--func_file", required=True, help="Input functional annotation JSON")
    parser.add_argument("--report", action="store_true", help="Show what change would be made")
    parser.add_argument("--update", action="store_true", help="Make the changes to the database")
    parser.add_argument(
        "--match_xrefs", action="store_true", help="Use xref IDs to match features if IDs do not work"
    )
    parser.add_argument("--version", action="version", version=ensembl.io.genomio.__version__)
    parser.add_log_arguments(add_log_file=True)
    args = parser.parse_args()
    init_logging_with_args(args)

    dbc = DBConnection(args.url)
    with dbc.session_scope() as session:
        load_descriptions(session, args.func_file, args.report, args.update, match_xrefs=args.match_xrefs)