Add reference selection functionality for multiref schemes (currently only artic-inrb-mpox)

artic/get_models.py

@@ -4,6 +4,7 @@
 import tarfile
 import sys
 from artic.utils import clair3_manifest
+from clint.textui import colored
 
 
 def download_file(url: str, local_path: Path):
@@ -18,6 +19,8 @@ def get_model(model_dir: Path, model_fname: str, model_url: str):
 
     model_path = Path(model_dir, model_fname)
 
+    os.makedirs(model_dir, exist_ok=True)
+
     download_file(model_url, model_path)
 
     with tarfile.open(model_path, "r") as tar:

artic/get_scheme.py

@@ -0,0 +1,50 @@
+from artic.utils import get_scheme
+from pathlib import Path
+
+
+def main():
+    import argparse
+    import os
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--scheme-name",
+        type=str,
+        required=True,
+        help="Name of the scheme you wish to fetch",
+    )
+    parser.add_argument(
+        "--scheme-version",
+        type=str,
+        required=True,
+        help="Version of the scheme you wish to fetch",
+    )
+    parser.add_argument(
+        "--scheme-directory",
+        type=Path,
+        help="Directory where schemes are stored",
+        default=f"{os.getcwd()}/primer-schemes",
+    )
+    parser.add_argument(
+        "--scheme-length",
+        type=str,
+        help="Length of the scheme to fetch, only required if the scheme has multiple possible lengths.",
+    )
+    parser.add_argument(
+        "--read-file",
+        type=Path,
+        help="FASTQ file containing reads sequenced with the scheme in question, this is only required when fetching a scheme with reference selection functionality.",
+    )
+    args = parser.parse_args()
+
+    get_scheme(
+        scheme_name=args.scheme_name,
+        scheme_version=args.scheme_version,
+        scheme_directory=args.scheme_directory,
+        scheme_length=args.scheme_length,
+        read_file=args.read_file,
+    )
+
+
+if __name__ == "__main__":
+    main()

artic/minion.py

@@ -49,7 +49,7 @@ def run(parser, args):
     else:
         if not os.getenv("CONDA_PREFIX"):
             print(
-                f"CONDA_PREFIX is not set, this probably means you are not running this inside a conda environment, please provide a model path argument '--model-path'",
+                "CONDA_PREFIX is not set, this probably means you are not running this inside a conda environment, please provide a model path argument '--model-path'",
                 file=sys.stderr,
             )
             raise SystemExit(1)
@@ -85,6 +85,7 @@ def run(parser, args):
             scheme_version=args.scheme_version,
             scheme_directory=args.scheme_directory,
             scheme_length=args.scheme_length,
+            read_file=args.read_file,
         )
 
     if not os.path.exists(bed) or not os.path.exists(ref):

artic/pipeline.py

@@ -129,7 +129,7 @@ def init_pipeline_parser():
     )
     remote_scheme_options.add_argument(
         "--scheme-length",
-        type=int,
+        type=str,
         metavar="scheme_length",
         default=False,
         help="Length of the scheme to fetch from the scheme repository (https://github.com/quick-lab/primerschemes). This is only required if the --scheme-name has multiple possible lengths.",