pygecko.gc_tools.sequence package

Submodules

pygecko.gc_tools.sequence.fid_sequence module

class pygecko.gc_tools.sequence.fid_sequence.FID_Sequence(metadata: dict | None, injections: dict[str, FID_Injection])

Bases: GC_Sequence

Class to represent FID sequences.

detector: None | str

injections: dict[slice(<class 'str'>, <class 'pygecko.gc_tools.injection.fid_injection.FID_Injection'>, None)]

instrument_name: str

internal_standard: Analyte | None

sequence_name: str

pygecko.gc_tools.sequence.gc_sequence module

class pygecko.gc_tools.sequence.gc_sequence.GC_Sequence(metadata: dict, injections: dict[slice(<class 'str'>, <class 'pygecko.gc_tools.injection.injection.Injection'>, None)])

Bases: object

Base class for all GC sequences.

sequence_name

Name of the sequence.

Type:: str

instrument_name

Name of the instrument the sequence was measured on.

Type:: str

injections

Injections of the sequence.

Type:: dict[str, Injection]

internal_standard

Internal standard of the sequence.

Type:: Analyte|None

detector: None | str

get_injection_by_pos(pos: str) → Injection: Returns the injection with the given plate position if positions are assigned to the injections. Raises an error if positions are not assigned.

injections: dict[str, Injection]

instrument_name: str

internal_standard: Analyte | None

pick_peaks(**kwargs): Picks peaks from the injections’ chromatograms. :param **kwargs: Keyword arguments for the peak picking.

save(filename: str) → None

Saves a GC sequence to a .pkl file.

Parameters:: filename (str) – Name of the file to save the sequence to.

sequence_name: str

set_internal_standard(rt: float | int, tolerance: float = 0.05, name: str | None = None, smiles: str | None = None) → None

Assigns the internal standard of the sequence to the corresponding peaks by creating an Analyte object for the internal standard and setting it as the peaks’ analyte.

Parameters:

rt (float|int) – Retention time of the internal standard.
tolerance (float) – Tolerance for the retention time matching. Default is 0.05.
name (str) – Name of the internal standard. Default is None.
smiles (str) – SMILES string of the internal standard. Default is None.

pygecko.gc_tools.sequence.gc_sequence.load_sequence(filename: str) → GC_Sequence

Loads a GC sequence from a .pkl file.

Parameters:: filename (str) – Name of the file to load the sequence from.
Returns:: GC_Sequence object loaded from the file.
Return type:: GC_Sequence

pygecko.gc_tools.sequence.gc_sequence.save_sequence(sequence: GC_Sequence, filename: str) → None

Saves a GC sequence to a .pkl file.

Parameters:: filename (str) – Name of the file to save the sequence to.

pygecko.gc_tools.sequence.ms_sequence module

class pygecko.gc_tools.sequence.ms_sequence.MS_Sequence(metadata: dict, injections: dict[slice(<class 'str'>, <class 'pygecko.gc_tools.injection.ms_injection.MS_Injection'>, None)])