refactor: move filtering technique to types

Author: JoshLoecker

main/como/rnaseq_gen.py

@@ -27,7 +27,7 @@
 
 from como.migrations import gene_info_migrations
 from como.project import Config
-from como.types import RNAPrepMethod
+from como.types import FilteringTechnique, RNAPrepMethod
 
 
 class _FilteringOptions(NamedTuple):
@@ -38,31 +38,6 @@ class _FilteringOptions(NamedTuple):
     high_batch_ratio: float
 
 
-class FilteringTechnique(Enum):
-    """RNA sequencing filtering capabilities."""
-
-    cpm = "cpm"
-    zfpkm = "zfpkm"
-    tpm = "quantile"
-    umi = "umi"
-
-    @staticmethod
-    def from_string(value: str) -> FilteringTechnique:
-        """Create a filtering technique object from a string."""
-        match value.lower():
-            case "cpm":
-                return FilteringTechnique.cpm
-            case "zfpkm":
-                return FilteringTechnique.zfpkm
-            case "quantile":
-                return FilteringTechnique.tpm
-            case "umi":
-                return FilteringTechnique.umi
-            case _:
-                possible_values = [t.value for t in FilteringTechnique]
-                raise ValueError(f"Got a filtering technique of '{value}'; should be one of: {possible_values}")
-
-
 class LayoutMethod(Enum):
     """RNA sequencing layout method."""
 

main/como/types.py

@@ -46,5 +46,30 @@ def from_string(value: str) -> RNAPrepMethod:
                 raise ValueError(f"Filtering technique must be one of {possible_values}; got: {value}")
 
 
+class FilteringTechnique(Enum):
+    """RNA sequencing filtering capabilities."""
+
+    cpm = "cpm"
+    zfpkm = "zfpkm"
+    tpm = "quantile"
+    umi = "umi"
+
+    @staticmethod
+    def from_string(value: str) -> FilteringTechnique:
+        """Create a filtering technique object from a string."""
+        match value.lower():
+            case "cpm":
+                return FilteringTechnique.cpm
+            case "zfpkm":
+                return FilteringTechnique.zfpkm
+            case "quantile":
+                return FilteringTechnique.tpm
+            case "umi":
+                return FilteringTechnique.umi
+            case _:
+                possible_values = [t.value for t in FilteringTechnique]
+                raise ValueError(f"Got a filtering technique of '{value}'; should be one of: {possible_values}")
+
+
 type_path = str | Path
 type_rna = Literal["total", "mrna"]