`pgfinder.validation`

Functions for validation of data.

Module Contents

`allowed_modifications`(→ list)	Loads allowable modifications from a csv file as a list.
`validate_raw_data_df`(→ None \| ValueError)	Validate that the raw data is a Pandas Dataframe with specific column names and that it has attributes.
`validate_theo_masses_df`(→ None \| ValueError)	Validate that the theoretical masses data is a Pandas Dataframe with specific column names and that it has
`validate_rt_window`(→ None \| ValueError)	Validate that rt_window is an float.
`validate_enabled_mod_list`(→ None \| ValueError)	Validate that enabled_mod_list is a list and modifications are allowed.
`validate_user_ppm`(→ None \| ValueError)	Validate that user_ppm is an integer.

pgfinder.validation.allowed_modifications(config_file: str | pathlib.Path = 'config/allowed_modifications.txt') → list[source]

Loads allowable modifications from a csv file as a list.

Parameters:: config_file (str | Path) – Path to a configuration file. Default ‘config/allowed_modifications.txt’
Returns:: List of permissible modifications.
Return type:: list

pgfinder.validation.validate_raw_data_df(raw_data_df: pandas.DataFrame, columns: dict = COLUMNS['pgfinder']) → None | ValueError[source]

Validate that the raw data is a Pandas Dataframe with specific column names and that it has attributes.

Parameters:: raw_data_df (pd.DataFrame) – Data frame to be validated.
Returns:: Error specific to the problem encountered with the data frame if any are encountered.
Return type:: None | ValueError
Raises:: ValueError –

pgfinder.validation.validate_theo_masses_df(theo_masses_df: pandas.DataFrame) → None | ValueError[source]

Validate that the theoretical masses data is a Pandas Dataframe with specific column names and that it has attributes.

Parameters:: raw_data_df (pd.DataFrame) – Data frame to be validated.
Returns:: Error specific to the problem encountered with the data frame if any are encountered.
Return type:: None | ValueError
Raises:: ValueError –

pgfinder.validation.validate_rt_window(rt_window: float) → None | ValueError[source]

Validate that rt_window is an float.

Parameters:: rt_window (int) – Value of rt_window to be validated.
Returns:: If no error nothing is returned, otherwise a ValueError is raised.
Return type:: None | ValueError
Raises:: ValueError –

pgfinder.validation.validate_enabled_mod_list(enabled_mod_list: list) → None | ValueError[source]

Validate that enabled_mod_list is a list and modifications are allowed.

Parameters:: enabled_mod_list (int) – Value of enabled_mod_list to be validated.
Returns:: If no error nothing is returned, otherwise a ValueError is raised.
Return type:: None | ValueError
Raises:: ValueError –

pgfinder.validation.validate_user_ppm(user_ppm: int) → None | ValueError[source]

Validate that user_ppm is an integer.

Parameters:: user_ppm (int) – Value of user_ppm to be validated.
Returns:: If no error nothing is returned, otherwise a ValueError is raised.
Return type:: None | ValueError
Raises:: ValueError –