Plate_reader

missense_kinase_toolkit/experiments/missense_kinase_toolkit/experiments/plate_reader.py

@@ -0,0 +1,117 @@
+import logging
+import xml.etree.ElementTree as ET
+from abc import ABC, abstractmethod
+from dataclasses import dataclass
+from datetime import datetime
+
+# i-control manual: https://bif.wisc.edu/wp-content/uploads/sites/389/2017/11/i-control_Manual.pdf
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class Measurement(ABC):
+    """Abstract class for measurements."""
+
+    filepath: str
+    """str: Filepath to i-control output .XML."""
+    label: str
+    """str: Label parameter in i-control."""
+
+    def __post_init__(self):
+        self.parse_for_section()
+        self.parse_for_time()
+
+    def parse_for_section(self):
+        try:
+            tree = ET.parse(self.filepath)
+            root = tree.getroot()
+            # TODO: check that i-control does not allow duplicate labels
+            self.section_element = root.find(f".//Section[@Name='{self.label}']")
+            if self.section_element is None:
+                logger.error("Label not found.")
+        except ET.ParseError as e:
+            logging.error(f"Could not parse input {self.filepath}", exc_info=e)
+
+    def parse_for_time(self):
+        self.time_start = datetime.fromisoformat(
+            self.section_element.find(".//Time_Start").text
+        )
+        self.time_end = datetime.fromisoformat(
+            self.section_element.find(".//Time_End").text
+        )
+
+    def get_parameter(self, parameter: str) -> str:
+        # TODO: Add units handling
+        parameter_attribute = self.section_element.find(
+            f".//Parameter[@Name='{parameter}']"
+        ).attrib["Value"]
+        return parameter_attribute
+
+    @abstractmethod
+    def get_data(self) -> int: ...
+
+    @abstractmethod
+    def plot_data(
+        self
+    ) -> Tuple[matplotlib.figure.Figure, plt.Axes] | None:
+    ...
+
+
+@dataclass
+class Luminescence_Scan(Measurement):
+    """Class to parse Luminescence Scan measurement."""
+
+    def get_data(self, cycle: int, temperature: int, well: str, wavelength: int):
+        data_element = self.section_element.find(
+            f".//Data[@Cycle='{str(cycle)}'][@Temperature='{str(temperature)}']"
+        )
+        if data_element is None:
+            logger.error("Data not found.")
+        else:
+            well_element = data_element.find(f".//Well[@Pos='{well}']")
+            scan_element = well_element.find(f".//Scan[@WL='{str(wavelength)}']")
+            return int(scan_element.text)
+
+    def plot_data(
+        cycle: int
+        temperature: int,
+        well: str,
+        header: str,
+        plot_type: str | None = None,
+    ):
+    if plot_type is None:
+        plot_type = "scatter"
+
+    list_plot_type = ["scatter"]
+    if plot_type not in list_plot_type:
+        logging.error(f"Plot type {plot_type} not yet supported...")
+        return None
+
+    if plot_type == "scatter":
+        lmin = int(self.get_parameter("Wavelength Start"))
+        lmax = int(self.get_parameter("Wavelength End"))
+        lstep = int(self.get_parameter("Wavelength Step Size"))
+        ll = np.arange(lmin, lmax+lstep, lstep)
+
+        fig, ax = plt.subplots()
+
+        try:
+            counter = 0
+            for l in ll:
+                ax.plot(l, self.get_data(cycle, temperature, well, l), "b.", alpha=0.5)
+                counter += 1
+            assert counter == int(self.get_parameter("Scan Number"))
+            print(f"All {counter} points accounted for")
+        except AssertionError as e:
+            logging.error(f"{counter} / {int(self.get_parameter('Scan Number'))} points accounted for...")
+            return None
+
+        ax.set_box_aspect(1)
+        ax.set_title("Water") # make this a parameter?
+        ax.set_xlabel("Wavelength (nm)")
+        ax.set_ylabel("Luminescence (RLU)")
+        ax.set_xlim([lmin, lmax])
+        ax.set_xticks(np.arange(lmin, lmax+50, 50)) # make this a parameter?
+
+        return (fig, ax)

missense_kinase_toolkit/experiments/pyproject.toml

@@ -5,6 +5,11 @@ description = "Tools to facilitate experimental analyses for missense_kinase_too
 authors = ["Jess White <[email protected]>"]
 license = "MIT"
 readme = "README.md"
+#https://safjan.com/the-importance-of-adding-py-typed-file-to-your-typed-package/
+packages = [
+    {include = "missense_kinase_toolkit"},
+    {include = "missense_kinase_toolkit/py.typed"}
+]
 
 [tool.poetry.dependencies]
 python = "^3.9"