Merge branch 'master' into issue-919-cnv-variant-query

Author: jonbrenas

malariagen_data/anoph/base_params.py

@@ -81,6 +81,13 @@
     """,
 ]
 
+cohort_group_query: TypeAlias = Annotated[
+    str,
+    """
+    A pandas query string to be evaluated against cohort-group metadata.
+    """,
+]
+
 sample_indices: TypeAlias = Annotated[
     List[int],
     """

malariagen_data/anoph/cnv_frq.py

@@ -586,7 +586,7 @@ def _gene_cnv_frequencies_advanced(
                 nobs[:, cohort_index] = np.repeat(cohort_n_called, 2)
             else:
                 assert nobs_mode == "fixed"
-                nobs[:, cohort_index] = cohort.size * 2
+                nobs[:, cohort_index] = cohort.size
 
         debug("compute frequency")
         with np.errstate(divide="ignore", invalid="ignore"):

malariagen_data/anoph/cohort_group_metadata.py

@@ -0,0 +1,60 @@
+from typing import Optional
+
+import pandas as pd
+from numpydoc_decorator import doc
+
+from ..util import _check_types
+from . import base_params
+from .base import AnophelesBase
+
+
+class AnophelesCohortGroupMetadata(AnophelesBase):
+    def __init__(
+        self,
+        **kwargs,
+    ):
+        # N.B., this class is designed to work cooperatively, and
+        # so it's important that any remaining parameters are passed
+        # to the superclass constructor.
+        super().__init__(**kwargs)
+
+    @_check_types
+    @doc(
+        summary="""
+            Read metadata for a specific cohort group, including cohort size,
+            country code, taxon, administrative units name, ISO code, geoBoundaries
+            shape ID and representative latitude and longitude points.
+        """,
+        parameters=dict(
+            cohort_group="""
+                A cohort group name. Accepted values are:
+                "admin1_month", "admin1_quarter", "admin1_year",
+                "admin2_month", "admin2_quarter", "admin2_year".
+            """
+        ),
+        returns="A dataframe of cohort metadata, one row per cohort.",
+    )
+    def cohort_group_metadata(
+        self,
+        cohort_group: base_params.cohorts,
+        cohort_group_query: Optional[base_params.cohort_group_query] = None,
+    ) -> pd.DataFrame:
+        major_version_path = self._major_version_path
+        cohorts_analysis = self.config.get("DEFAULT_COHORTS_ANALYSIS")
+
+        path = f"{major_version_path[:2]}_cohorts/cohorts_{cohorts_analysis}/cohorts_{cohort_group}.csv"
+
+        # Read the manifest into a pandas dataframe.
+        with self.open_file(path) as f:
+            df_cohorts = pd.read_csv(f, sep=",", na_values="")
+
+        # Ensure all column names are lower case.
+        df_cohorts.columns = [c.lower() for c in df_cohorts.columns]
+
+        # Apply a cohort group selection.
+        if cohort_group_query is not None:
+            # Assume a pandas query string.
+            df_cohorts = df_cohorts.query(cohort_group_query)
+            df_cohorts = df_cohorts.reset_index(drop=True)
+
+        return df_cohorts.copy()