Improve usage and meteor downloader

meteor/downloader.py

@@ -22,12 +22,17 @@
 from time import time
 import tarfile
 import json
+from typing import ClassVar
+import sys
 
 
 @dataclass
 class Downloader(Session):
     """Download and prepare catalogues"""
 
+    CONFIG_DATA_FILE: ClassVar[Path] = Path("data/zenodo.json")
+    TEST_CATALOGUE: ClassVar[str] = "test"
+
     meteor: type[Component]
     choice: str
     taxonomy: bool
@@ -36,14 +41,26 @@
     catalogues_config: dict = field(default_factory=dict)
     start_time: float = field(default_factory=float)
 
-    def __post_init__(self) -> None:
+    @staticmethod
+    def load_catalogues_config() -> dict:
         try:
-            config_data = importlib.resources.files("meteor") / "data/zenodo.json"
+            config_data = importlib.resources.files("meteor") / str(Downloader.CONFIG_DATA_FILE)
             with importlib.resources.as_file(config_data) as configuration_path:
                 with configuration_path.open("rt", encoding="UTF-8") as config:
-                    self.catalogues_config = json.load(config)
-        except AssertionError:
-            logging.error("The file zenodo.json is missing in meteor source")
+                    return json.load(config)
+        except FileNotFoundError:
+            logging.error("The file %s is missing in meteor source", Downloader.CONFIG_DATA_FILE.name)
+            sys.exit(1)
+
+    @staticmethod
+    def get_available_catalogues() -> list[str]:
+        catalogues_config = Downloader.load_catalogues_config()
+        available_catalogues = list(catalogues_config.keys())
+        available_catalogues.remove(Downloader.TEST_CATALOGUE)
+        return available_catalogues
+
+    def __post_init__(self) -> None:
+        self.catalogues_config = Downloader.load_catalogues_config()
         self.meteor.ref_dir.mkdir(exist_ok=True, parents=True)
         if self.taxonomy:
             self.data_type = "taxonomy_info"
@@ -111,7 +128,7 @@
             )
             urlretrieve(url, filename=catalogue, reporthook=self.show_progress)
             print(flush=True)
-            if self.choice == "test":
+            if self.choice == Downloader.TEST_CATALOGUE:
                 for sample in self.catalogues_config[self.choice]["samples"]:
                     logging.info(f"Download {sample} fastq file")
                     url_fastq = self.catalogues_config[self.choice]["samples"][sample][
@@ -140,3 +157,4 @@
             )
         except AssertionError:
             logging.error("MD5sum of %s has a different value than expected", catalogue)
+            sys.exit(1)

meteor/meteor.py

@@ -148,18 +148,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         dest="user_choice",
         type=str,
         required=True,
-        choices=[
-            "cat_gut",
-            "chicken_caecal",
-            "dog_gut",
-            "human_gut",
-            "human_oral",
-            "human_skin",
-            "mouse_gut",
-            "rabbit_gut",
-            "rat_gut",
-            "pig_gut",
-        ],
+        choices=Downloader.get_available_catalogues(),
         help="Select the catalogue to download.",
     )
     download_parser.add_argument(
@@ -231,7 +220,6 @@ def get_arguments() -> Namespace:  # pragma: no cover
     fastq_parser.add_argument(
         "-p",
         dest="ispaired",
-        default=False,
         action="store_true",
         help="Fastq files are paired.",
     )
@@ -542,10 +530,10 @@ def get_arguments() -> Namespace:  # pragma: no cover
         dest="max_depth",
         default=100,
         type=int,
-        help="Maximum depth taken in account (default 100).",
+        help="Maximum depth taken in account (default: %(default)d).",
     )
     strain_parser.add_argument(
-        "-t", dest="threads", default=1, type=int, help="Threads count."
+        "-t", dest="threads", default=1, type=num_threads, help="Threads count."
     )
     # strain_parser.add_argument(
     #     "-c",
@@ -561,7 +549,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         choices=range(1, 10000),
         metavar="MIN_SNP_DEPTH",
         type=int,
-        help="""Minimum snp depth (default >=3).
+        help="""Minimum snp depth (default: >= %(default)d).
         Values should be comprised between 1 and the maximum depth
         (10000 reads are taken in account).""",
     )
@@ -570,7 +558,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         dest="min_frequency_non_reference",
         default=0.8,
         type=isborned01,
-        help="Minimum frequency for non reference allele (default >=0.8).",
+        help="Minimum frequency for non reference allele (default: >= %(default).1f).",
     )
     strain_parser.add_argument(
         "-m",
@@ -579,7 +567,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         choices=range(1, 101),
         metavar="MIN_MSP_COVERAGE",
         type=int,
-        help="""Minimum number of genes from the MSP that are covered (default >=50).
+        help="""Minimum number of genes from the MSP that are covered (default: >= %(default)d).
         Values should be comprised between 1 and 100
         (maximum number of core genes taken in account).""",
     )
@@ -588,7 +576,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         dest="min_gene_coverage",
         default=0.8,
         type=isborned01,
-        help="Minimum gene coverage from 0 to 1 (default >=0.5).",
+        help="Minimum gene coverage from 0 to 1 (default: >= %(default).1f).",
     )
     strain_parser.add_argument(
         "-o",
@@ -601,7 +589,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         "--kc",
         dest="keep_consensus",
         action="store_true",
-        help="Keep consensus marker genes (default False, set to True to recompute strain)",
+        help="Keep consensus marker genes (default: False, set to True to recompute strain)",
     )
     strain_parser.add_argument(
         "--tmp",
@@ -624,36 +612,36 @@ def get_arguments() -> Namespace:  # pragma: no cover
         dest="max_gap",
         default=0.5,
         type=isborned01,
-        help="Removes sites constitued of >= cutoff gap character (default >=0.5).",
+        help="Removes sites constitued of >= cutoff gap character (default: >= %(default).1f).",
     )
     tree_parser.add_argument(
         "-c",
         dest="gap_char",
         default="-",
         type=str,
-        help="Gap character (default -).",
+        help="Gap character (default: %(default)s).",
     )
     tree_parser.add_argument(
         "-f",
         dest="format",
         default=None,
         choices=["png", "svg", "pdf", "txt"],
         type=str,
-        help="Output image format (default txt).",
+        help="Output image format (default: %(default)s).",
     )
     tree_parser.add_argument(
         "-w",
         dest="width",
         default=500,
         type=int,
-        help="Output image width (default 500px).",
+        help="Output image width (default: %(default)dpx).",
     )
     tree_parser.add_argument(
         "-H",
         dest="height",
         default=500,
         type=int,
-        help="Output image height (default 500px).",
+        help="Output image height (default: %(default)dpx).",
     )
     tree_parser.add_argument(
         "-o",
@@ -663,7 +651,7 @@ def get_arguments() -> Namespace:  # pragma: no cover
         help="Path to output directory.",
     )
     tree_parser.add_argument(
-        "-t", dest="threads", default=1, type=int, help="Threads count."
+        "-t", dest="threads", default=num_threads, type=int, help="Threads count."
     )
     tree_parser.add_argument(
         "--tmp",
@@ -679,10 +667,10 @@ def main() -> None:  # pragma: no cover
     """
     Main program function
     """
-    # Get arguments
-    args = get_arguments()
     # Let us logging
     logger = get_logging()
+    # Get arguments
+    args = get_arguments()
     # version = importlib.metadata.version("meteor")
     # print("Meteor version", version)
     # Create a meteor dataset
@@ -809,7 +797,7 @@ def main() -> None:  # pragma: no cover
             meteor.tmp_dir = Path(tmpdirname)
             meteor.mapping_dir = Path(tmpdirname) / "map"
             meteor.fastq_dir = Path(tmpdirname)
-            downloader = Downloader(meteor, "test", False, True)
+            downloader = Downloader(meteor, Downloader.TEST_CATALOGUE, False, True)
             downloader.execute()
             fastq_importer = FastqImporter(meteor, meteor.tmp_dir, False, None)
             fastq_importer.execute()

meteor/treebuilder.py

@@ -23,7 +23,7 @@
 import sys
 import pandas as pd
 import lzma
-
+from shutil import rmtree
 
 @dataclass
 class TreeBuilder(Session):
@@ -121,3 +121,4 @@
                     )
             except ete3.parser.newick.NewickError:
                 logging.info("Not sufficient info in %s.", str(tree_file.resolve()))
+        rmtree(self.meteor.tmp_dir, ignore_errors=True)