pygecko.parsers package

Submodules

pygecko.parsers.agilent_fid_parser module

class pygecko.parsers.agilent_fid_parser.Agilent_FID_Parser

Bases: object

A class wrapping functions to parse raw data from an Agilent GC/FID into FID_Sequence objects.

classmethod load_injection(raw_directory: str, solvent_delay: float | int) → FID_Injection

Returns an FID_Injection object.

Parameters:

• raw_directory (str) – Path to the directory containing the corresponding xy-file and the acaml-file.

• solvent_delay (float) – Retention time of the solvent peak in minutes.

Returns:

An FID_Injection object.

Return type:

FID_Injection

classmethod load_ri_calibration(raw_directory: str, solvent_delay, c_count: int, rt: float) → RI_Calibration

Returns an RI_Calibration object.

Parameters:

• raw_directory (str) – Path to the directory containing the corresponding xy-file and the acaml-file.

• solvent_delay (float) – Retention time of the solvent peak in minutes.

• c_count (int) – Carbon count of the alkane the retention time is provided for.

• rt (float) – Retention time of the alkane the c_count is provided for.

Returns:

An RI_Calibration object.

Return type:

RI_Calibration

classmethod load_sequence(raw_directory: str, solvent_delay: float | int, pos: bool = False) → FID_Sequence

Returns an FID_Sequence object.

Parameters:

• raw_directory (str) – Path to the directory containing the corresponding xy-files and the acaml-file.

• solvent_delay (float) – Retention time of the solvent peak in minutes.

• pos (bool, optional) – Indicates if plate position is given in the injection names. Defaults to False.

Returns:

An FID_Sequence object

Return type:

FID_Sequence

pygecko.parsers.agilent_ms_parser module

class pygecko.parsers.agilent_ms_parser.Agilent_MS_Parser

Bases: object

A class wrapping functions to parse raw data from an Agilent GC/MS into MS_Sequence objects.

classmethod load_injection(raw_directory: str) → MS_Injection

Returns an MS_Injection object.

Parameters:

raw_directory (str) – Path to the directory containing the raw data.

Returns:

An MS_Injection object

Return type:

MS_Injection

classmethod load_ri_calibration(raw_directory: str, c_count: int, rt: float) → RI_Calibration

Returns an RI_Calibration object.

Parameters:

• raw_directory (str) – Path to the directory containing the raw data.

• c_count (int) – Number of carbon atoms for as specific alkane present in the standard.

• rt (float) – Retention time of the alkane the c_count is provided for.

Returns:

An RI_Calibration object

Return type:

RI_Calibration

classmethod load_sequence(sequence_directory: str, pos: bool = False) → MS_Sequence

Returns an MS_Sequence object.

Parameters:

• sequence_directory (str) – Path to the directory containing the raw data.

• chrom_path (str) – Path to the directory containing the chromatograms.

• pos (bool, optional) – Indicates if plate position is given in the injection names. Defaults to False.

Returns:

An MS_Sequence object

Return type:

MS_Sequence

pygecko.parsers.fid_base_parser module

class pygecko.parsers.fid_base_parser.FID_Base_Parser

Bases: object

static load_injection(xy_file: Path | str, solvent_delay: float, pos: bool = False) → FID_Injection

Returns an FID_Injection object.

Parameters:

• xy_file (Path|str) – Path to a xy_file.

• solvent_delay (float) – Solvent delay of the injection.

Returns:

An FID_Injection object.

Return type:

FID_Injection

static load_ri_calibration(xy_file: Path | str, solvent_delay, c_count: int, rt: float) → RI_Calibration

Returns an RI_Calibration object.

Parameters:

• xy_file (Path|str) – Path to a xy_file.

• solvent_delay (float) – Solvent delay of the injection.

• c_count (int) – Carbon count of the alkane the retention time is provided for.

• rt (float) – Retention time of the alkane the c_count is provided for.

Returns:

An RI_Calibration object.

Return type:

RI_Calibration

static load_sequence(xy_directory: Path | str, solvent_delay: float, pos: bool = False) → FID_Sequence

Returns an FID_Sequence object.

Parameters:

• xy_directory (Path|str) – Path to a directory containing xy-files.

• solvent_delay (float) – Solvent delay of the injections.

Returns:

An FID_Sequence object.

Return type:

FID_Sequence

static read_xy_array(path: Path) → ndarray | None

Takes in the path to a xy-file, returns the xy_array.

pygecko.parsers.file_readers module

pygecko.parsers.file_readers.extract_scans_from_mzml(mzml_file: ~pathlib.Path) -> (<class 'pandas.core.frame.DataFrame'>, <class 'str'>)

Takes in the path to a mzml file containing the scans of an injection, returns a DataFrame containing the scans and the sample name.

Parameters:

mzml_file (Path) – Path to the mzml file.

Returns:

DataFrame containing the scans and the sample name.

Return type:

tuple[pd.DataFrame, str]

pygecko.parsers.file_readers.extract_scans_from_mzxml(mzxml_file: Path) → DataFrame

Takes in the path to a mzxml file containing the scans of an injection, returns a DataFrame containing the scans and the sample name.

Parameters:

mzxml_file (Path) – Path to the mzxml file.

Returns:

DataFrame containing the scans and the sample name.

Return type:

tuple[pd.DataFrame, str]

pygecko.parsers.ms_base_parser module

class pygecko.parsers.ms_base_parser.MS_Base_Parser

Bases: object

static extract_scans_from_raw_data(raw_path: ~pathlib.Path, temp_dir: ~tempfile.TemporaryDirectory | None = None) -> (<class 'pandas.core.frame.DataFrame'>, <class 'str'>)

Takes in the path to a raw file containing the scans of an injection, returns a DataFrame containing the scans and the injection’s sample name.

static initialize_injection(path: Path, pos: bool = False, temp_dir: TemporaryDirectory | None = None) → MS_Injection

Returns an MS_Injection object.

Parameters:

path (Path) – Path to the raw directory.

Returns:

An MS_Injection object

Return type:

MS_Injection

static load_injection(raw_data_path: str | Path, pos: bool = False, temp_dir: TemporaryDirectory | None = None) → MS_Injection

Returns an MS_Injection object.

Parameters:

• raw_data_path (str) – Path to the raw data.

• temp_dir (tempfile.TemporaryDirectory) – Temporary directory to store the converted mzML file. Defaults to None.

Returns:

An MS_Injection object

Return type:

MS_Injection

static load_ri_calibration(raw_data_path: str, c_count: int, rt: float) → RI_Calibration

Returns an RI_Calibration object.

Parameters:

• raw_directory (str) – Path to the directory containing the raw data.

• c_count (int) – Number of carbon atoms for as specific alkane present in the standard.

• rt (float) – Retention time of the alkane the c_count is provided for.

Returns:

An RI_Calibration object

Return type:

RI_Calibration

static load_sequence(raw_directory: Path | str, pos: bool = False) → MS_Sequence

Returns an MS_Sequence object.

Parameters:

raw_directory (Path|str) – Path to a directory containing raw data.

Returns:

An MS_Sequence object.

Return type:

MS_Sequence

pygecko.parsers.msconvert_wraper module

pygecko.parsers.msconvert_wraper.msconvert(input_files: list | str, output_dir, format='mzML')

Takes in a list of input filenames and the output directory, converts the input files to the specified format and saves them in the output directory.

Parameters:

• input_files (list|str) – Input filename or list of input filenames.

• output_dir (str) – Path to the output directory.

• format (str) – Output format. Default: ‘mzML’.

pygecko.parsers.utilities module

class pygecko.parsers.utilities.HiddenPrints

Bases: object

pygecko.parsers.utilities.find_directories_with_extension(directory_path, extension)

pygecko.parsers.utilities.list_files_and_directories(directory_path)

Module contents