MSDataOutput

class MSDataOutput.MSDataOutput(output_directory, input_file_path, result_name='Results', logger=None, ingui=True)

A class to describe the general setup for Data Output.

Parameters:

• output_directory (str) – directory path to output the data

• input_file_path (str) – file path of the input MRM transition name file. To be used for the output filename

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

transpose_MSdata(allow_multiple_istd=False)

Function to transpose data

Parameters:

• MS_df (pandas DataFrame) – A panda data frame

• allow_multiple_istd (bool) – if True, display the Transition_Name_ISTD as well besides the Transition_Name

Returns:

MS_df (pandas DataFrame) – A panda data frame with data transposed

start_writer()

Function to open a writer object

df_to_file_preparation(df, transpose=False, logger=None, ingui=False, allow_multiple_istd=False)

Function to check and set up the settings needed before writing to a file.

Parameters:

• output_option (str) – the Output_Options value given to MSOrganiser.

• df (pandas DataFrame) – A panda data frame to output

• transpose (bool) – if True, transpose the dataframe first before writing to the Excel sheet

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

• allow_multiple_istd (bool) – if True, display the Transition_Name_ISTD as well besides the Transition_Name

Returns:

(list) –

list containing:

• df (pandas DataFrame): A panda data frame to output. Transposed if transpose is set to True

• output_option (str): Updated output options if changes are required E.g S/N to S_to_N

df_to_file(output_option, df, transpose=False, allow_multiple_istd=False)

Funtion to write a df to a csv file named {input file name}_{output_option}_{result filename}.csv .

Parameters:

• output_option (str) – the name of the result csv file. MSOrganiser puts it as the Output_Options value

• df (pandas DataFrame) – A panda data frame to output to csv

• transpose (bool) – if True, transpose the dataframe first before writing to the Excel sheet

• allow_multiple_istd (bool) – if True, display the Transition_Name_ISTD as well besides the Transition_Name

Note

For the output option S/N, it will be changed to S_to_N as filenames does not accept slashes. This is done in the function df_to_file_preparation

class MSDataOutput.MSDataOutput_csv(output_directory, input_file_path, result_name='Results', logger=None, ingui=True)

A class to describe the general setup for Data Output to csv.

Parameters:

• output_directory (str) – directory path to output the data

• input_file_path (str) – file path of the input MRM transition name file. To be used for the output filename

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

df_to_file(output_option, df, transpose=False, allow_multiple_istd=False)

Funtion to write a df to an excel file.

Parameters:

• output_option (str) – the name of the sheet

• df (pandas DataFrame) – A panda data frame to output to Excel

• transpose (bool) – if True, transpose the dataframe first before writing to the Excel sheet

• allow_multiple_istd (bool) – if True, display the Transition_Name_ISTD as well besides the Transition_Name

Note

For the output option S/N, it will be changed to S_to_N as excel does not accept slashes. This is done in the function df_to_file_preparation

class MSDataOutput.MSDataOutput_Excel(output_directory, input_file_path, result_name='Results', logger=None, ingui=True)

A class to describe the general setup for Data Output to Excel.

Parameters:

• output_directory (str) – directory path to output the data

• input_file_path (str) – file path of the input MRM transition name file. To be used for the output filename

• logger (object) – logger object created by start_logger in MSOrganiser

• ingui (bool) – if True, print analysis status to screen

start_writer()

Function to open an Excel writer object using openpyxl

end_writer(testing=False)

Function to close an Excel writer object

df_to_file(output_option, df, transpose=False, allow_multiple_istd=False)

Funtion to write a df to an excel file.

Parameters:

• output_option (str) – the name of the sheet

• df (pandas DataFrame) – A panda data frame to output to Excel

• transpose (bool) – if True, transpose the dataframe first before writing to the Excel sheet

• allow_multiple_istd (bool) – if True, display the Transition_Name_ISTD as well besides the Transition_Name

Note

For the output option S/N, it will be changed to S_to_N as excel does not accept slashes. This is done in the function df_to_file_preparation