feat: remove fetch (moved to vrs anvil toolkit)

src/vrsix/cli.py

@@ -7,9 +7,6 @@
 import click
 
 from vrsix import load as load_vcf
-from vrsix.fetch import fetch_by_pos_range as vcf_fetch_by_pos_range
-from vrsix.fetch import fetch_by_vrs_ids
-from vrsix.output import generate_csv
 
 _logger = logging.getLogger(__name__)
 
@@ -56,73 +53,3 @@ def load(vcfs: tuple[Path], db_location: Path | None) -> None:
         load_vcf.load_vcf(vcf, db_location)
         end = timer()
         _logger.info("Processed `%s` in %s seconds", vcf, end - start)
-
-
-@cli.command()
-@click.argument(
-    "vrs-ids",
-    nargs=-1,
-)
-@click.option(
-    "--db-location",
-    type=click.Path(
-        file_okay=True, dir_okay=True, readable=True, writable=True, path_type=Path
-    ),
-)
-@click.option(
-    "-o",
-    "--output",
-    type=click.Path(readable=True, writable=True, path_type=Path),
-)
-def fetch_by_id(
-    vrs_ids: list[str], db_location: Path | None, output: Path | None
-) -> None:
-    """Fetch VCF positions by VRS ID"""
-    if not vrs_ids:
-        return
-    rows = fetch_by_vrs_ids(vrs_ids, db_location)
-    if output:
-        generate_csv(rows, output)
-    else:
-        for row in rows:
-            click.echo(",".join(row))
-
-
-@cli.command()
-@click.argument("chrom", required=True)
-@click.argument(
-    "start",
-    type=click.INT,
-    required=True,
-)
-@click.argument(
-    "end",
-    type=click.INT,
-    required=True,
-)
-@click.option(
-    "--db-location",
-    type=click.Path(
-        file_okay=True, dir_okay=True, readable=True, writable=True, path_type=Path
-    ),
-)
-@click.option(
-    "-o",
-    "--output",
-    type=click.Path(readable=True, writable=True, path_type=Path),
-)
-def fetch_by_range(
-    chrom: str, start: int, end: int, db_location: Path | None, output: Path | None
-) -> None:
-    """Fetch VCF rows by position range.
-
-    :param chrom: chromosome
-    :param start: starting position
-    :param end: ending position
-    """
-    rows = vcf_fetch_by_pos_range(chrom, start, end, db_location)
-    if output:
-        generate_csv(rows, output)
-    else:
-        for row in rows:
-            click.echo(",".join(row))