RIAssigner.data

Submodules

Classes

`Data`	Base class for data managers.
`PandasData`	Class to handle data from filetypes which can be imported into a pandas dataframe.
`MatchMSData`	Class to handle data from filetypes which can be imported
`SimpleData`	Class to handle data from numpy arrays
`ValidateSimpleData`	Class to handle data from numpy arrays

Package Contents

class RIAssigner.data.Data(filename: str, filetype: str, rt_unit: str)[source]

Bases: abc.ABC

Base class for data managers.

RetentionTimeType

RetentionIndexType

CommentFieldType

URegistry

_keys_conversions

_rt_possible_keys

_ri_possible_keys

static is_valid(value: RetentionTimeType | RetentionIndexType) → bool[source]

Determine whether a retention time value is valid

Parameters:: rt (RetentionTimeType) – Value to check for validity.
Returns:: State of validity (True/False).
Return type:: bool

static can_be_float(rt: pint.Quantity | float | int) → bool[source]

Determine whether a value can be converted to a float.

This function checks if the provided input is an instance of either Quantity, float, or int.

Parameters:: rt (Union[Quantity, float, int]) – Value to check for float conversion.
Returns:: True if the input is an instance of Quantity, float, or int, False otherwise.
Return type:: bool

classmethod add_possible_rt_keys(keys: List[str]) → None[source]

A method that adds new identifiers to get retention time information.

Parameters:: keys (List[str]) – A list of new identifiers (keys) to be added to the _rt_possible_keys.
Returns:: None

classmethod add_possible_ri_keys(keys: List[str]) → None[source]

A method that adds new identifiers to get retention index information.

Parameters:: keys (List[str]) – A list of new identifiers (keys) to be added to the _ri_possible_keys.
Returns:: None

classmethod get_possible_rt_keys() → List[str][source]

A method that returns the possible keys to get retention times.

Returns:: A list of possible keys to get retention times.
Return type:: List[str]

classmethod get_possible_ri_keys() → List[str][source]

A method that returns the possible keys to get retention indices.

Returns:: A list of possible keys to get retention indices.
Return type:: List[str]

_filename

_filetype

_rt_unit

_unit

abstractmethod write(filename: str) → None[source]

Store current content to disk.

Parameters:: filename (str) – Path to output filename.

property filename: str

Getter for filename property.

Returns:: Filename of originally loaded data.
Return type:: str

property retention_times: Iterable[RetentionTimeType]

Abstractmethod:

Getter for retention_times property.

Returns:: RT values contained in data.
Return type:: Iterable[RetentionTimeType]

property retention_indices: Iterable[RetentionIndexType]

Abstractmethod:

Getter for retention_indices property.

Returns:: RI values stored in data.
Return type:: Iterable[RetentionIndexType]

has_retention_indices() → bool[source]

Check if all retention indices in the spectra exist.

This method iterates over the retention indices in the spectra. If it encounters a value that is None, it immediately returns False. If it iterates over all retention indices without finding a None value, it returns True.

Returns:: True if all retention indices exist, False otherwise.
Return type:: bool

has_retention_times() → bool[source]

Check if all retention times in the spectra exist.

This method iterates over the retention times in the spectra. If it encounters a value that is None, it immediately returns False. If it iterates over all retention times without finding a None value, it returns True.

Returns:: True if all retention times exist, False otherwise.
Return type:: bool

property comment: Iterable[CommentFieldType]

Abstractmethod:

Getter for comment property.

Returns:: Comment field values stored in data.
Return type:: Iterable[CommentFieldType]

init_ri_from_comment(ri_source: str) → None[source]

Extract RI from comment field. Extracts the RI from the comment field of the data file. The RI is expected to be in the format ‘ri_source=RI_value’. The function extracts the RI value and sets it on the retention_index property.

Parameters:

content_comment – Comment field of the data file.
ri_source – String that is expected to be in the comment field before the RI value.

class RIAssigner.data.PandasData(filename: str, filetype: str, rt_unit: str)[source]

Bases: RIAssigner.data.Data.Data

Class to handle data from filetypes which can be imported into a pandas dataframe.

_carbon_number_column_names

_rt_key = 'rt'

_read()[source]: Load content from file into PandasData object.

_read_into_dataframe() → None[source]: Read the data from file into dataframe.

write(filename: str) → None[source]: Write data on disk. Supports ‘csv’, ‘tsv’, ‘tabular’ and ‘parquet’ formats.

_init_carbon_number_index() → None[source]: Find key of carbon number column and store it.

_init_rt_column_info() → None[source]: Find key of retention time column and store it.

_init_ri_column_info() → None[source]: Initialize retention index column name and set its position next to the retention time column.

_init_ri_indices() → None[source]: Initialize retention indices to a factor of 100 of carbon numbers or None if carbon numbers are not present.

_sort_by_rt() → None[source]: Sort peaks by their retention times.

_replace_nans_with_0s() → None[source]: Replace NaN values (including blank strings and invalid values) with 0s.

__eq__(o: object) → bool[source]

Comparison operator ==.

Parameters:: o (object) – Object to compare with.
Returns:: State of equality.
Return type:: bool

property retention_times: Iterable[RIAssigner.data.Data.Data.RetentionTimeType]: Get retention times in seconds.

property retention_indices: Iterable[RIAssigner.data.Data.Data.RetentionIndexType]: Get retention indices from data or computed from carbon numbers.

_ri_from_carbon_numbers() → Iterable[int][source]: Returns the RI of compound based on carbon number.

property comment: Iterable[RIAssigner.data.Data.Data.CommentFieldType]

Get comments.

Returns:: Comments.
Return type:: Iterable[Data.CommentFieldType]

class RIAssigner.data.MatchMSData(filename: str, filetype: str, rt_unit: str)[source]

Bases: RIAssigner.data.Data.Data

Class to handle data from filetypes which can be imported using ‘matchms’.

_read()[source]: Load data into object and initialize properties.

write(filename: str) → None[source]

Write data to back to the spectra file

Parameters:: filename (str) – Path to filename under which to store the data.

_write_RIs_to_spectra() → None[source]: Write the RI values stored in the object to the spectra metadata.

_read_retention_times() → None[source]: Read retention times from spectrum metadata.

_read_retention_indices() → None[source]: Read retention indices from spectrum metadata.

_sort_spectra_by_rt() → None[source]: Sort objects (peaks) in spectra list by their retention times.

__eq__(o: object) → bool[source]

Comparison operator ==.

Parameters:: o (object) – Object to compare with.
Returns:: State of equality.
Return type:: bool

property retention_times: Iterable[RIAssigner.data.Data.Data.RetentionTimeType]: Get retention times in seconds.

property retention_indices: Iterable[RIAssigner.data.Data.Data.RetentionIndexType]: Get retention indices.

property comment: Iterable[RIAssigner.data.Data.Data.CommentFieldType]: Get comments.

property spectra_metadata: Tuple[numpy.array, List[str]]

class RIAssigner.data.SimpleData(retention_times: Iterable[float], rt_unit: str, retention_indices: Iterable[float] = None)[source]

Bases: RIAssigner.data.Data.Data

Class to handle data from numpy arrays

_read(retention_times, retention_indices)[source]

abstractmethod write()[source]

Store current content to disk.

Parameters:: filename (str) – Path to output filename.

property retention_indices: Iterable[RIAssigner.data.Data.Data.RetentionIndexType]

Getter for retention_indices property.

Returns:: RI values stored in data.
Return type:: Iterable[RetentionIndexType]

property retention_times: Iterable[RIAssigner.data.Data.Data.RetentionTimeType]

Getter for retention_times property.

Returns:: RT values contained in data.
Return type:: Iterable[RetentionTimeType]

property comment: Iterable[str | None]

Getter for comment property.

Returns:: Comment field values stored in data.
Return type:: Iterable[CommentFieldType]

class RIAssigner.data.ValidateSimpleData(retention_times: Iterable[float], rt_unit: str, retention_indices: Iterable[float] = None)[source]

Bases: RIAssigner.data.SimpleData.SimpleData

Class to handle data from numpy arrays

_validate_input(retention_times, retention_indices)[source]