add relabel cli to combineapp

Author: nebfield

pgscatalog.combineapp/pyproject.toml

@@ -22,7 +22,8 @@ requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.scripts]
-pgscatalog-combine = 'pgscatalog.combineapp.cli:run'
+pgscatalog-combine = 'pgscatalog.combineapp.combine_cli:run'
+pgscatalog-relabel = 'pgscatalog.combineapp.relabel_cli:run'
 
 [tool.pytest.ini_options]
 minversion = "6.0"

pgscatalog.combineapp/src/pgscatalog/combineapp/__init__.py

@@ -1,3 +1,3 @@
-from pgscatalog.combineapp.cli import run
+from pgscatalog.combineapp.combine_cli import run
 
 __all__ = ["run"]

pgscatalog.combineapp/src/pgscatalog/combineapp/cli.py pgscatalog.combineapp/src/pgscatalog/combineapp/combine_cli.py

@@ -0,0 +1,107 @@
+import argparse
+import logging
+import pathlib
+
+from pgscatalog.corelib import relabel, relabel_write, RelabelArgs
+
+logger = logging.getLogger(__name__)
+
+
+def _parse_args(args=None):
+    parser = argparse.ArgumentParser(
+        description="Relabel the column values in one file based on a pair of columns in another",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+    parser.add_argument(
+        "-d",
+        "--dataset",
+        dest="dataset",
+        required=True,
+        help="<Required> Label for target genomic dataset",
+    )
+    parser.add_argument(
+        "-m",
+        "--maps",
+        help="mapping filenames",
+        dest="map_files",
+        nargs="+",
+        required=True,
+    )
+    parser.add_argument(
+        "-o", "--outdir", help="output directory", dest="outdir", required=True
+    )
+    parser.add_argument(
+        "--col_from", help="column to change FROM", dest="col_from", required=True
+    )
+    parser.add_argument(
+        "--col_to", help="column to change TO", dest="col_to", required=True
+    )
+    parser.add_argument(
+        "--target_file", help="target file", dest="target_file", required=True
+    )
+    parser.add_argument(
+        "--target_col",
+        help="target column to revalue",
+        dest="target_col",
+        required=True,
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        dest="verbose",
+        action="store_true",
+        help="<Optional> Extra logging information",
+    )
+    parser.add_argument("--split", dest="split", action="store_true", required=False)
+    parser.add_argument(
+        "--combined", dest="combined", action="store_true", required=False
+    )
+    parser.add_argument("-cc", "--comment_char", dest="comment_char", default="##")
+    args = parser.parse_args()
+
+    if not (args.split or args.combined):
+        parser.error("At least one of --combined or --split is required")
+
+    return args
+
+
+def run():
+    args = _parse_args()
+
+    if args.verbose:
+        logging.getLogger("pgscatalog.corelib").setLevel(logging.DEBUG)
+        logger.setLevel(logging.DEBUG)
+        logger.debug("Verbose logging enabled")
+
+    relabel_args = RelabelArgs(
+        comment_char=args.comment_char,
+        dataset=args.dataset,
+        map_col_from=args.col_from,
+        map_col_to=args.col_to,
+        target_col=args.target_col,
+    )
+    logger.debug(f"Relabel arguments {relabel_args}")
+
+    map_paths = [pathlib.Path(x) for x in args.map_files]
+    in_path = pathlib.Path(args.target_file)
+
+    for x in [*map_paths, in_path]:
+        if not x.exists():
+            raise FileNotFoundError(f"{x}")
+
+    logger.debug("Relabelling variants")
+    relabelled = relabel(
+        in_path=in_path, map_paths=map_paths, relabel_args=relabel_args
+    )
+    logger.debug(f"Writing relabelled data to {args.outdir}")
+    relabel_write(
+        relabelled=relabelled,
+        dataset=relabel_args.dataset,
+        split_output=args.split,
+        combined_output=args.combined,
+        out_dir=args.outdir,
+    )
+
+
+if __name__ == "__main__":
+    run()

pgscatalog.combineapp/src/pgscatalog/combineapp/relabel_cli.py

@@ -5,7 +5,7 @@
 from unittest.mock import patch
 import pytest
 
-from pgscatalog.combineapp.cli import run
+from pgscatalog.combineapp.combine_cli import run
 from pgscatalog.corelib import ScoringFile
 
 

pgscatalog.combineapp/tests/test_cli.py pgscatalog.combineapp/tests/test_combine_cli.py

@@ -0,0 +1,67 @@
+import csv
+import itertools
+import os
+from unittest.mock import patch
+
+import pytest
+from xopen import xopen
+
+from pgscatalog.combineapp.relabel_cli import run
+
+
+@pytest.fixture(scope="package")
+def map_files(request):
+    return [
+        str(request.path.parent / "testdata" / "relabel_map_chr1.txt.gz"),
+        str(request.path.parent / "testdata" / "relabel_map_chr8.txt.gz"),
+    ]
+
+
+@pytest.fixture(scope="package")
+def relabel_scorefile(request):
+    return str(request.path.parent / "testdata" / "hgdp_ALL_additive_0.scorefile")
+
+
+def test_relabel(tmp_path_factory, relabel_scorefile, map_files):
+    """Test relabelling a scorefile."""
+    out_dir = tmp_path_factory.mktemp("outdir")
+
+    args = [
+        ("pgscatalog-relabel", "-m"),
+        map_files,
+        (
+            "--target_file",
+            relabel_scorefile,
+            "--target_col",
+            "ID",
+            "-d",
+            "hgdp",
+            "--col_from",
+            "ID_TARGET",
+            "--col_to",
+            "ID_REF",
+            "-o",
+            str(out_dir),
+            "--combined",
+            "--split",
+        ),
+    ]
+    flargs = list(itertools.chain(*args))
+
+    with patch("sys.argv", flargs):
+        run()
+
+    out_f = os.listdir(out_dir)
+    assert sorted(out_f) == [
+        "hgdp_1_relabelled.gz",
+        "hgdp_8_relabelled.gz",
+        "hgdp_ALL_relabelled.gz",
+    ]
+
+    for x in out_f:
+        with xopen(out_dir / x) as f:
+            reader = csv.DictReader(f, delimiter="\t")
+            for line in reader:
+                assert "ID" in line
+                assert "effect_allele" in line
+                assert "PGS000802_hmPOS_GRCh38" in line

pgscatalog.combineapp/tests/test_relabel_cli.py

@@ -0,0 +1,3 @@
+ID	effect_allele	PGS000802_hmPOS_GRCh38
+1:11796321:G:A	A	0.16
+8:127401060:G:T	G	0.217