CoreMS 4.0.0__py3-none-any.whl

corems/mass_spectra/input/massList.py

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+__author__ = "Yuri E. Corilo"
+__date__ = "Jun 12, 2019"
+
+import sys
+
+from pathlib import Path
+from threading import Thread
+import warnings
+from corems.mass_spectrum.input.massList import ReadCoremsMasslist
+from corems.mass_spectra.factory.lc_class import LCMSBase
+
+
+class ReadCoremsMassSpectraText(ReadCoremsMasslist, Thread):
+    """
+    Class for reading CoreMS mass spectra from a text file.
+
+    Parameters
+    ----------
+    file_location : str, pathlib.Path, or s3path.S3Path
+        Path object from pathlib containing the file location
+    analyzer : str, optional
+        Name of the analyzer, by default 'Unknown'
+    instrument_label : str, optional
+        Label of the instrument, by default 'Unknown'
+
+    Attributes
+    ----------
+    lcms : LCMSBase
+        LCMSBase object for storing the mass spectra data.
+
+    Methods
+    -------
+    * get_scans_filename(). Get the filenames of all the scan files associated with the CoreMS file.
+    * set_filepath_datatype_and_delimiter(file_path_obj). Set the file path, data type, and delimiter based on the file path object.
+    * import_mass_spectra(). Import the mass spectra from the scan files and add them to the LCMSBase object.
+    * run(). Run the import_mass_spectra method to create the LCMSBase object.
+    * get_lcms_obj(). Get the LCMSBase object.
+    """
+
+    def __init__(self, file_location, analyzer="Unknown", instrument_label="Unknown"):
+        if isinstance(file_location, str):
+            # if obj is a string it defaults to create a Path obj, pass the S3Path if needed
+            file_location = Path(file_location)
+
+        if not file_location.exists():
+            raise FileNotFoundError("%s not found" % file_location)
+
+        if not file_location.suffix == ".corems":
+            raise TypeError("%s is not a valid CoreMS file" % file_location)
+
+        Thread.__init__(self)
+
+        ReadCoremsMasslist.__init__(self, file_location)
+
+        self.lcms = LCMSBase(
+            self.file_location, analyzer=analyzer, instrument_label=instrument_label
+        )
+
+    def get_scans_filename(self) -> list:
+        all_other = self.file_location.glob("*_scan*[!.json]")
+
+        scans_filepath = [
+            (file_path_obj.stem.split("scan")[1], file_path_obj)
+            for file_path_obj in all_other
+        ]
+
+        scans_filepath.sort(key=lambda m: int(m[0]))
+
+        return scans_filepath
+
+    def set_filepath_datatype_and_delimiter(self, file_path_obj) -> None:
+        self.file_location = file_path_obj
+
+        if file_path_obj.suffix == ".pkl":
+            self.data_type == "dataframe"
+
+        else:
+            if file_path_obj.suffix == ".csv":
+                self.data_type == "txt"
+                self.delimiter = ","
+
+            elif file_path_obj.suffix == ".xlsx":
+                self.data_type == "excel"
+                self.delimiter = ","
+
+            elif file_path_obj.suffix == ".txt":
+                self.data_type == "txt"
+                self.delimiter = "\t"
+                warnings.warn("using tab as delimiter")
+            else:
+                raise NotImplementedError(
+                    "%s data not yet supported " % file_path_obj.suffix
+                )
+
+    def import_mass_spectra(self) -> None:
+        list_rt, list_tic, list_scan = list(), list(), list()
+
+        for scan_number, file_path_obj in self.get_scans_filename():
+            self.set_filepath_datatype_and_delimiter(file_path_obj)
+
+            mass_spec = self.get_mass_spectrum(int(scan_number))
+
+            list_scan.append(int(scan_number))
+
+            list_rt.append(mass_spec.retention_time)
+
+            list_tic.append(mass_spec.tic)
+
+            self.lcms.add_mass_spectrum(mass_spec)
+
+        self.lcms.retention_time = list_rt
+        self.lcms.tic_list = list_tic  # TODO: check if this is correct
+        self.lcms.scans_number = list_scan
+
+    def run(self) -> None:
+        """Creates the LCMS object and imports mass spectra."""
+
+        self.import_mass_spectra()
+
+    def get_lcms_obj(self) -> LCMSBase:
+        """
+        Returns the LCMSBase object associated with the massList.
+
+        If the LCMSBase object is already initialized, it is returned.
+        Otherwise, an exception is raised.
+
+        Raises:
+            Exception: If the LCMSBase object is not initialized.
+        """
+        if self.lcms:
+            return self.lcms
+        else:
+            raise Exception("returning an empty lcms class")