quantion 0.1.6__py3-none-win_amd64.whl

quantion/__init__.py

@@ -0,0 +1,156 @@
+from __future__ import annotations
+
+from quantion._bridge import _ABI, load_library
+from quantion import api as _api
+from quantion.api import (
+    parse_mzml,
+    parse_ion,
+    ion_to_mzml,
+    mzml_to_ion,
+    mzml_to_ion_file,
+    calculate_eic,
+    get_scans,
+    find_peaks,
+    get_peak,
+    fit_peak,
+    draw_peak,
+    find_noise_level,
+    calculate_baseline,
+    get_peaks_from_eic,
+    get_peaks_from_chrom,
+    find_features,
+    find_feature,
+    get_features,
+    load_model,
+    load_warp,
+)
+from quantion.file import SampleFile
+from quantion.model import Model
+from quantion.warp_model import WarpModel
+from quantion._pack import pack_peak_options, encode_target_ids, unpack_targets
+from quantion._shared import to_cores
+from quantion._types import FromTo, GroupedFeature, Feature, Peak, Target, TargetPeak
+
+__version__ = "0.1.6"
+
+__all__ = [
+    "Quantion",
+    "parse_mzml",
+    "parse_ion",
+    "ion_to_mzml",
+    "mzml_to_ion",
+    "mzml_to_ion_file",
+    "calculate_eic",
+    "get_scans",
+    "find_peaks",
+    "get_peak",
+    "fit_peak",
+    "draw_peak",
+    "find_noise_level",
+    "calculate_baseline",
+    "get_peaks_from_eic",
+    "get_peaks_from_chrom",
+    "find_features",
+    "find_feature",
+    "get_features",
+    "SampleFile",
+    "load_model",
+    "load_warp",
+    "Model",
+    "WarpModel",
+    "FromTo",
+    "Target",
+    "Peak",
+    "TargetPeak",
+    "Feature",
+    "GroupedFeature",
+    "pack_peak_options",
+    "encode_target_ids",
+    "unpack_targets",
+    "to_cores",
+]
+
+
+class Quantion:
+    def __init__(self, abi: _ABI) -> None:
+        self._abi = abi
+        _api._set_abi(abi)
+
+    def parse_mzml(self, data: bytes) -> SampleFile:
+        return parse_mzml(data)
+
+    def parse_ion(self, source, max_cache_size: int = 0) -> SampleFile:
+        return parse_ion(source, max_cache_size)
+
+    def ion_to_mzml(self, file: SampleFile) -> str:
+        return ion_to_mzml(file)
+
+    def mzml_to_ion(self, file: SampleFile, level: int = 12, f32_compress: bool = False) -> bytes:
+        return mzml_to_ion(file, level, f32_compress)
+
+    def mzml_to_ion_file(self, input_path: str, output_path: str, level: int = 12, f32_compress: bool = False) -> None:
+        return mzml_to_ion_file(input_path, output_path, level, f32_compress)
+
+    def calculate_eic(self, file: SampleFile, target_mz: float, from_to: FromTo, ppm_tol: float = 20.0, mz_tol: float = 0.005):
+        return calculate_eic(file, target_mz, from_to, ppm_tol, mz_tol)
+
+    def get_scans(self, file: SampleFile, *, rt_range=None, rt=None, mz_range=None, mz=None, level: int = 1):
+        return get_scans(file, rt_range=rt_range, rt=rt, mz_range=mz_range, mz=mz, level=level)
+
+    def find_peaks(self, x, y, options=None):
+        return find_peaks(x, y, options)
+
+    def get_peak(self, x, y, rt: float, range: float, options=None):
+        return get_peak(x, y, rt, range, options)
+
+    def fit_peak(self, x, y, rt: float, intensity: float, shape: str = "emg"):
+        return fit_peak(x, y, rt, intensity, shape)
+
+    def draw_peak(self, x, params):
+        return draw_peak(x, params)
+
+    def find_noise_level(self, y) -> dict:
+        return find_noise_level(y)
+
+    def calculate_baseline(self, y, lambda_: int = 0, max_iterations: int = 0):
+        return calculate_baseline(y, lambda_, max_iterations)
+
+    def get_peaks_from_eic(self, file: SampleFile, targets, from_to: FromTo = {"from": 0.5, "to": 5.0}, options=None, cores: int = 1):
+        return get_peaks_from_eic(file, targets, from_to, options, cores)
+
+    def get_peaks_from_chrom(self, file: SampleFile, items, options=None, cores: int = 1):
+        return get_peaks_from_chrom(file, items, options, cores)
+
+    def find_features(self, file: SampleFile, from_to: FromTo, *, eic=None, grid=None, options=None, cores: int = 1):
+        return find_features(file, from_to, eic=eic, grid=grid, options=options, cores=cores)
+
+    def find_feature(self, file: SampleFile, targets, *, scan_eic=None, eic=None, options=None, cores: int = 1):
+        return find_feature(file, targets, scan_eic=scan_eic, eic=eic, options=options, cores=cores)
+
+    def get_features(self, directory_path: str, from_to: FromTo, *, eic=None, grid=None, grouping=None, options=None, cores: int = 1):
+        return get_features(directory_path, from_to, eic=eic, grid=grid, grouping=grouping, options=options, cores=cores)
+
+    def load_model(self, source) -> Model:
+        return load_model(source)
+
+    def load_warp(self, model: Model) -> WarpModel:
+        return load_warp(model)
+
+    def __repr__(self) -> str:
+        return "<Quantion ready>"
+
+
+def __getattr__(name):
+    if name == "MsUtils":
+        import warnings
+        warnings.warn(
+            "MsUtils is renamed to Quantion and will be removed in the next breaking release",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return Quantion
+    raise AttributeError(name)
+
+
+_, _abi = load_library()
+_api._set_abi(_abi)