pygecko.analysis package

Submodules

pygecko.analysis.analysis module

class pygecko.analysis.analysis.Analysis

Bases: object

A class wrapping functions to analyze GC data.

static calc_plate_conv(ms_sequence: MS_Sequence, fid_sequence: FID_Sequence, layout: Reaction_Array, path: str | None = None, index: int = 0, **kwargs) → ndarray

Matches GC-MS and GC-FID peaks and quantifies the conversion of the reactions.

Parameters:

  • ms_sequence (MS_Sequence) – MS_Sequence object containing the GC-MS data.

  • fid_sequence (FID_Sequence) – FID_Sequence object containing the GC-FID data.

  • layout (Reaction_Array) – Well_Plate object containing the combinatorial reaction layout.

  • path (str|None, optional) – Path to write the results to. Defaults to None.

Returns:

Numpy array containing the quantification results, retention times and smiles for the analytes.

Return type:

np.ndarray

static calc_plate_yield(ms_sequence: MS_Sequence, fid_sequence: FID_Sequence, layout: Reaction_Array | Product_Array, path: str | None = None, **kwargs) → ndarray

Matches GC-MS and GC-FID peaks and quantifies the yields of the reactions.

Parameters:

  • ms_sequence (MS_Sequence) – MS_Sequence object containing the GC-MS data.

  • fid_sequence (FID_Sequence) – FID_Sequence object containing the GC-FID data.

  • layout (Reaction_Array|Product_Array) – Reaction_Array or Product_Array object containing the reaction

  • layout.

  • path (str|None, optional) – Path to write the results to. Defaults to None.

Returns:

Numpy array containing the quantification results, retention times and smiles for the analytes.

Return type:

np.ndarray

static fit_calibration_curve(fid_sequence: FID_Sequence, analyte: Analyte, ratios: list[float], intercept: bool = False) → tuple[float, float]

Fits a calibration curve to the analyte in a FID sequence using scikit-learn.

Parameters:

  • fid_sequence (FID_Sequence) – FID_Sequence object containing the GC-FID data.

  • analyte (Analyte) – Analyte to fit the calibration curve to.

  • ratios (list[float]) – List of concentration ratios for calibration.

  • intercept (bool) – If True, fit intercept (default True). If False, force through origin.

Returns:

(slope, intercept) of calibration curve.

Return type:

tuple[float, float]

static match_mz_plate(ms_sequence: MS_Sequence, layout: Reaction_Array, path: str | None = None, return_canidates: bool = True, check_iso: bool = False, **kwargs) → DataFrame

Matches m/z values of the MS peaks to the analytes in the reaction layout. :param ms_sequence: MS_Sequence object containing the GC-MS data. :param layout: Reaction_Array object containing the combinatorial reaction layout. :param path: (str|None): Path to write the results to. Defaults to None. :param **kwargs: Additional keyword arguments to pass to the match_mol method.

Returns:

DataFrame containing the m/z values, retention times and smiles for the analytes.

Return type:

pd.DataFrame

static quantify_analyte(fid_sequence: FID_Sequence, rt_analyte: float, analyte: Analyte | None = None, method='polyarc', path: str | None = None, **kwargs) → dict

Returns the yields of Analytes at a given retention time in a FID sequence.

Parameters:

  • fid_sequence (FID_Sequence) – FID_Sequence object containing the GC-FID data.

  • rt (float) – Retention time to quantify the Analytes at.

  • analyte (Analyte) – Analyte to quantify.

  • method (str) – Method to use for quantification. Defaults to ‘polyarc’ can be set to calibration to use calibration curve.

  • path (str|None) – Path to write the results to. Defaults to None.

Returns:

Dictionary containing the yields of the Analytes in the FID sequence.

Return type:

dict

static quantify_plate(fid_sequence: FID_Sequence, rt_analyte: float, analyte: Analyte | None = None, method='polyarc', path: str | None = None, **kwargs) → ndarray

Returns the yields of Analytes at a given retention time in the FID sequence of a plate.

Parameters:

  • fid_sequence (FID_Sequence) – FID_Sequence object containing the GC-FID data.

  • rt (float) – Retention time to quantify the Analytes at.

  • analyte (Analyte) – Analyte to quantify.

  • method (str) – Method to use for quantification. Defaults to ‘polyarc’ can be set to calibration to use calibration curve.

  • path (str|None) – Path to write the results to. Defaults to None.

Returns:

Array containing the yields of the Analytes in the FID sequence.

Return type:

np.ndarray

Module contents