clophfit.prtecan.models#

Prtecan/prtecan.py.

Classes#

`Labelblock`	Parse a label block.
`Tecanfile`	Parse a Tecan .xls file.
`LabelblocksGroup`	Group labelblocks with compatible metadata.
`TecanfilesGroup`	Group of Tecanfiles containing at least one common Labelblock.
`PlateScheme`	Define buffer, discard, ctrl and unk wells, and ctrl names.

Module Contents#

class clophfit.prtecan.models.Labelblock#

Parse a label block.

Parameters:

lines

Raises:

ValueError – When data do not correspond to a complete 96-well plate.
TypeError – When normalization parameters are not numerical.

Notes

Logs a warning when it replaces “OVER” with np.nan for saturated values.

lines: dataclasses.InitVar[list[list[str | int | float]]]#: Lines to create this Labelblock.

filename: str = ''#: Path of the corresponding Tecan file.

metadata: dict[str, clophfit.prtecan.parsers.Metadata]#: Metadata specific for this Labelblock.

data: dict[str, float]#: Plate data values as {‘well_name’, value}.

data_nrm: dict[str, float]#: Plate data values normalized as {‘well_name’, value}.

almost_equal(other)#

Check if two Labelblocks are almost equal (same excitation and emission).

Parameters:: other (Labelblock)
Return type:: bool

class clophfit.prtecan.models.Tecanfile#

Parse a Tecan .xls file.

Parameters:

path (Path) – Path to .xls file.

Raises:

FileNotFoundError – When path does not exist.
ValueError – When no Labelblock is found or file format is invalid.

metadata: dict[str, clophfit.prtecan.parsers.Metadata]#: General metadata for Tecanfile, like Date and Shaking Duration.

labelblocks: dict[int, Labelblock]#: All labelblocks contained in this file.

class clophfit.prtecan.models.LabelblocksGroup#

Group labelblocks with compatible metadata.

Parameters:

labelblocks (list[Labelblock]) – Labelblocks to be grouped.
allequal

Raises:

Exception – When labelblocks are neither equal nor almost equal.

allequal: bool = False#: True if labelblocks already tested equal.

metadata: dict[str, clophfit.prtecan.parsers.Metadata]#: Metadata shared by all labelblocks.

property data: dict[str, list[float]]#

Grouped data if labelblocks are equal, otherwise empty.

Return type:: dict[str, list[float]]

property data_nrm: dict[str, list[float]]#

Normalized data by number of flashes, integration time and gain.

Return type:: dict[str, list[float]]

class clophfit.prtecan.models.TecanfilesGroup#

Group of Tecanfiles containing at least one common Labelblock.

Parameters:: tecanfiles (list[Tecanfile]) – List of Tecanfiles.
Raises:: ValueError – When no common Labelblock is found across all Tecanfiles.

Notes

Logs a warning if the Tecanfiles do not contain the same number of Labelblocks that can be merged in the same order. In such cases, fewer LabelblocksGroup may be created.

labelblocksgroups: dict[int, LabelblocksGroup]#: Each group contains its own data like a titration.

metadata: dict[str, clophfit.prtecan.parsers.Metadata]#: Metadata shared by all tecanfiles.

class clophfit.prtecan.models.PlateScheme#

Define buffer, discard, ctrl and unk wells, and ctrl names.

Parameters:: file (Path) – File path to the scheme file [<well Id, sample name>].

property nofit_keys: set[str]#

Buffer and discarded wells.

Return type:: set[str]

property buffer: list[str]#

List of buffer wells.

Return type:: list[str]

property discard: list[str]#

List of discard wells.

Return type:: list[str]

property ctrl: list[str]#

List of CTR wells.

Return type:: list[str]

property names: dict[str, set[str]]#

A dictionary mapping sample names to their associated list of wells.

Return type:: dict[str, set[str]]