Check normalization and tree output format

metagenopolis · Apr 2, 2024 · 3c57656 · 3c57656
1 parent 16c34ae
commit 3c57656
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git a/meteor/mapper.py b/meteor/mapper.py
@@ -33,8 +33,8 @@ class Mapper(Session):
     """Run the bowtie"""
 
     DEFAULT_NUM_THREADS : ClassVar[int] = 1
-    MAPPING_TYPES: ClassVar[list[str]] = ['end-to-end', 'local']
-    DEFAULT_MAPPING_TYPE: ClassVar[str] = 'end-to-end'
+    MAPPING_TYPES: ClassVar[list[str]] = ["end-to-end", "local"]
+    DEFAULT_MAPPING_TYPE: ClassVar[str] = "end-to-end"
     DEFAULT_TRIM: ClassVar[int] = 80
     NO_TRIM: ClassVar[int] = 0
     DEFAULT_ALIGNMENT_NUMBER: ClassVar[int] = 10000

diff --git a/meteor/profiler.py b/meteor/profiler.py
@@ -33,7 +33,7 @@ class Profiler(Session):
     NO_RAREFACTION: ClassVar[int] = 0
     DEFAULT_RAREFACTION_LEVEL: ClassVar[int] = NO_RAREFACTION
     DEFAULT_RANDOM_SEED: ClassVar[int] = 1234
-    NORMALIZATIONS: ClassVar[list[str]] = ["coverage", "fpkm", "raw"]
+    NORMALIZATIONS: ClassVar[list[str|None]] = [None, "coverage", "fpkm", "raw"]
     DEFAULT_NORMALIZATION: ClassVar[str] = "coverage"
     DEFAULT_COVERAGE_FACTOR: ClassVar[float] = 100.0
     DEFAULT_CORE_SIZE: ClassVar[int] = 100
@@ -50,6 +50,9 @@ class Profiler(Session):
     coverage_factor: float
 
     def __post_init__(self):
+        if self.normalization not in Profiler.NORMALIZATIONS:
+            raise ValueError(f'{self.normalization} is not a valid normalization')
+
         # Get the json file
         self.sample_config = self.get_census_stage(self.meteor.mapping_dir, 1)
 

diff --git a/meteor/tests/test_profiler.py b/meteor/tests/test_profiler.py
@@ -31,7 +31,7 @@ def profiler_standard(datadir: Path, tmp_path: Path) -> Profiler:
         rarefaction_level=-1,
         seed=12345,
         coverage_factor=100.0,
-        normalization="",
+        normalization=None,
         core_size=4,
         msp_filter=0.5,
         completeness=0.6,

diff --git a/meteor/treebuilder.py b/meteor/treebuilder.py
@@ -32,7 +32,7 @@ class TreeBuilder(Session):
 
     DEFAULT_MAX_GAP: ClassVar[float] = 0.5
     DEFAULT_GAP_CHAR: ClassVar[str] = "-"
-    OUTPUT_FORMATS: ClassVar[list[str]] = ["png", "svg", "pdf", "txt"]
+    OUTPUT_FORMATS: ClassVar[list[str|None]] = [None, "png", "svg", "pdf", "txt"]
     DEFAULT_OUTPUT_FORMAT: ClassVar[str|None] = None
     DEFAULT_WIDTH: ClassVar[int] = 500
     DEFAULT_HEIGHT: ClassVar[int] = 500
@@ -46,6 +46,9 @@ class TreeBuilder(Session):
     gap_char: str
 
     def __post_init__(self) -> None:
+        if self.format not in TreeBuilder.OUTPUT_FORMATS:
+            raise ValueError(f'{self.format} is not a valid output format')
+
         self.meteor.tmp_dir = Path(mkdtemp(dir=self.meteor.tmp_path))
         self.meteor.tree_dir.mkdir(exist_ok=True, parents=True)