sai-pg 1.0.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

sai/preprocessors/feature_preprocessor.py

@@ -0,0 +1,236 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+import numpy as np
+from pathlib import Path
+from typing import Any
+from sai.preprocessors import DataPreprocessor
+from sai.registries.stat_registry import STAT_REGISTRY
+from sai.configs import PloidyConfig, StatConfig
+
+
+class FeaturePreprocessor(DataPreprocessor):
+    """
+    A preprocessor subclass for generating feature vectors from genomic data.
+
+    This class extends DataPreprocessor to include additional functionality for creating
+    feature vectors based on genomic variants, reference and target individual genotypes,
+    and window-based genomic statistics.
+    """
+
+    def __init__(
+        self,
+        output_file: str,
+        stat_config: StatConfig,
+        anc_allele_available: bool = False,
+    ):
+        """
+        Initializes FeatureVectorsPreprocessor with specific frequency thresholds
+        and output file for storing generated feature vectors.
+
+        Parameters
+        ----------
+        output_file : str
+            Path to the output file to save processed feature vectors.
+        stat_config: StatConfig,
+            Specifies the configuration of statistics to compute.
+        anc_allele_available: bool, optional
+            If True, ancestral allele information is available.
+            If False, ancestral allele information is unavailable.
+            Default is False.
+        """
+        self.output_file = output_file
+        self.anc_allele_available = anc_allele_available
+        self.stat_config = stat_config
+
+    def run(
+        self,
+        chr_name: str,
+        ref_pop: str,
+        tgt_pop: str,
+        src_pop_list: list[str],
+        start: int,
+        end: int,
+        pos: np.ndarray,
+        ref_gts: np.ndarray,
+        tgt_gts: np.ndarray,
+        src_gts_list: list[np.ndarray],
+        ploidy_config: PloidyConfig,
+    ) -> list[dict[str, Any]]:
+        """
+        Generates feature vectors for a specified genomic window.
+
+        Parameters
+        ----------
+        chr_name : str
+            Chromosome name.
+        ref_pop : str
+            Reference population name.
+        tgt_pop : str
+            Target population name.
+        src_pop_list : list[str]
+            List of source population names.
+        start : int
+            Start position of the genomic window.
+        end : int
+            End position of the genomic window.
+        pos : np.ndarray
+            A 1D numpy array where each element represents the genomic position.
+        ref_gts : np.ndarray
+            Genotype data for the reference population.
+        tgt_gts : np.ndarray
+            Genotype data for the target population.
+        src_gts_list : list[np.ndarray]
+            List of genotype arrays for each source population.
+        ploidy_config: PloidyConfig
+            Configuration specifying ploidy levels for each population involved in the analysis.
+
+        Returns
+        -------
+        list[dict[str, Any]]
+            A list containing a dictionary of calculated feature vectors for the genomic window.
+        """
+        items = {
+            "chr_name": chr_name,
+            "start": start,
+            "end": end,
+            "ref_pop": ref_pop,
+            "tgt_pop": tgt_pop,
+            "src_pop_list": src_pop_list,
+            "nsnps": len(pos),
+            "cdd_pos": {},
+        }
+
+        if (
+            (ref_gts is None)
+            or (tgt_gts is None)
+            or (src_gts_list is None)
+            or (ploidy_config is None)
+        ):
+            for stat_name in self.stat_config.root.keys():
+                if len(src_pop_list) > 1:
+                    items[stat_name] = [np.nan for _ in range(len(src_pop_list))]
+                else:
+                    items[stat_name] = np.nan
+                if stat_name in ["U", "Q"]:
+                    items[stat_name] = np.nan
+                    items["cdd_pos"][stat_name] = np.array([])
+        else:
+            for stat_name in self.stat_config.root.keys():
+                stat_cls = STAT_REGISTRY.get(stat_name)
+                stat = stat_cls(
+                    ref_gts=ref_gts,
+                    tgt_gts=tgt_gts,
+                    src_gts_list=src_gts_list,
+                    ref_ploidy=ploidy_config.get_ploidy("ref", ref_pop),
+                    tgt_ploidy=ploidy_config.get_ploidy("tgt", tgt_pop),
+                    src_ploidy_list=ploidy_config.get_ploidy("src"),
+                )
+                if stat_name == "U":
+                    results = stat.compute(
+                        pos=pos,
+                        w=self.stat_config.get_parameters(stat_name)["ref"][ref_pop],
+                        x=self.stat_config.get_parameters(stat_name)["tgt"][tgt_pop],
+                        y_list=list(
+                            self.stat_config.get_parameters(stat_name)["src"].values()
+                        ),
+                        anc_allele_available=self.anc_allele_available,
+                    )
+                    items["cdd_pos"][stat_name] = results["cdd_pos"]
+                elif stat_name == "Q":
+                    results = stat.compute(
+                        pos=pos,
+                        w=self.stat_config.get_parameters(stat_name)["ref"][ref_pop],
+                        quantile=self.stat_config.get_parameters(stat_name)["tgt"][
+                            tgt_pop
+                        ],
+                        y_list=list(
+                            self.stat_config.get_parameters(stat_name)["src"].values()
+                        ),
+                        anc_allele_available=self.anc_allele_available,
+                    )
+                    items["cdd_pos"][stat_name] = results["cdd_pos"]
+                else:
+                    results = stat.compute()
+                items[stat_name] = results["value"]
+
+        return [items]
+
+    def process_items(self, items: list[dict[str, Any]]) -> None:
+        """
+        Processes and writes a single dictionary of feature vectors to the output file.
+
+        Parameters
+        ----------
+        items : dict[str, Any]
+            A dictionary containing feature vectors for a genomic window.
+        """
+        with open(
+            self.output_file, "a"
+        ) as f:  # Open in append mode for continuous writing
+            lines = []
+            for item in items:
+                src_pop = item["src_pop_list"]
+                src_pop_str = ",".join(src_pop)
+
+                stats_parts = []
+                for stat_name in self.stat_config.root.keys():
+                    val = item.get(stat_name)
+
+                    if isinstance(val, list) and len(val) == len(src_pop):
+                        # expand one value per src, in the same order as src_pop
+                        stats_parts.extend("" if v is None else str(v) for v in val)
+                    else:
+                        # fallback: single value
+                        if isinstance(val, list):
+                            v = val[0] if len(val) > 0 else ""
+                        else:
+                            v = val
+                        stats_parts.append("" if v is None else str(v))
+
+                stats = "\t".join(stats_parts)
+
+                line = (
+                    f"{item['chr_name']}\t{item['start']}\t{item['end']}\t"
+                    f"{item['ref_pop']}\t{item['tgt_pop']}\t{src_pop_str}\t"
+                    f"{item['nsnps']}\t{stats}\n"
+                )
+                lines.append(line)
+
+            f.writelines(lines)
+
+        for key in ("U", "Q"):
+            if key in self.stat_config.root:
+                path = Path(self.output_file)
+                log_file = path.with_suffix(f".{key}.log")
+                with open(log_file, "a") as f:
+                    lines = []
+                    for item in items:
+                        cdd = (
+                            "NA"
+                            if item["cdd_pos"][key].size == 0
+                            else ",".join(
+                                f"{item['chr_name']}:{pos}"
+                                for pos in item["cdd_pos"][key]
+                            )
+                        )
+                        line = f"{item['chr_name']}\t{item['start']}\t{item['end']}\t{cdd}\n"
+                        lines.append(line)
+                    f.writelines(lines)

sai/registries/__init__.py

@@ -0,0 +1,22 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+from .generic_registry import GenericRegistry
+from .stat_registry import StatRegistry

sai/registries/generic_registry.py

@@ -0,0 +1,89 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+from abc import ABC, abstractmethod
+from typing import Any, Callable
+
+
+class GenericRegistry(ABC):
+    """
+    Generic class for all registries.
+
+    Provides a consistent interface for registering and retrieving
+    named components such as missions, models, or features.
+    """
+
+    def __init__(self):
+        self._registry = {}
+
+    def register(self, name: str) -> Callable:
+        """
+        Decorator to register a class or callable under a given name.
+
+        Parameters
+        ----------
+        name : str
+            The key under which the component is registered.
+
+        Returns
+        -------
+        Callable
+            A decorator that registers the class/function.
+        """
+
+        def decorator(obj: Any) -> Any:
+            self._register(name, obj)
+            return obj
+
+        return decorator
+
+    def _register(self, name: str, obj: Any) -> None:
+        if name in self._registry:
+            raise ValueError(f"{name!r} is already registered.")
+        self._registry[name] = obj
+
+    def get(self, name: str) -> Any:
+        """
+        Retrieves a registered component by name.
+
+        Parameters
+        ----------
+        name : str
+            The key of the registered component.
+
+        Returns
+        -------
+        Any
+            The registered component.
+        """
+        if name not in self._registry:
+            raise KeyError(f"No component registered under name '{name}'")
+        return self._registry[name]
+
+    def list_registered(self) -> list[str]:
+        """
+        Lists all registered component names.
+
+        Returns
+        -------
+        list of str
+            Names of all registered components.
+        """
+        return list(self._registry.keys())

sai/registries/stat_registry.py

@@ -0,0 +1,30 @@
+# Copyright 2025 Xin Huang
+#
+# GNU General Public License v3.0
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, please see
+#
+#    https://www.gnu.org/licenses/gpl-3.0.en.html
+
+
+from sai.registries.generic_registry import GenericRegistry
+
+
+class StatRegistry(GenericRegistry):
+    """
+    Concrete registry for statistic classes.
+    """
+
+
+STAT_REGISTRY = StatRegistry()