rcx_tk.sequence
===============

.. py:module:: rcx_tk.sequence


Functions
---------

.. autoapisummary::

   rcx_tk.sequence.process_sequence_file
   rcx_tk.sequence.process_sequence
   rcx_tk.sequence.cleanup
   rcx_tk.sequence.validate_injection_order
   rcx_tk.sequence.derive_additional_metadata
   rcx_tk.sequence.rearrange_columns
   rcx_tk.sequence.validate_filenames_column
   rcx_tk.sequence.add_local_order
   rcx_tk.sequence.add_sequence_identifier
   rcx_tk.sequence.separate_filename
   rcx_tk.sequence.add_subject_identifier


Module Contents
---------------

.. py:function:: process_sequence_file(file_path: str, out_path: str) -> None

   Processes a metadata file, keeping and renaming specific columns.

   :param file_path: A path to the metadata file.
   :type file_path: str
   :param out_path: A path where processed metadata dataframe is exported.
   :type out_path: str


.. py:function:: process_sequence(df: pandas.DataFrame) -> pandas.DataFrame

   Processes the metadata dataframe.

   :param df: The metadata dataframe.
   :type df: pd.DataFrame

   :returns: A metadata dataframe with rearranged and newly derived columns.
   :rtype: pd.DataFrame


.. py:function:: cleanup(df: pandas.DataFrame) -> pandas.DataFrame

   Removes the file Name column and moves the sampleName col.

   :param df: The metadata dataframe.
   :type df: pd.DataFrame

   :returns: The processed dataframe.
   :rtype: pd.DataFrame


.. py:function:: validate_injection_order(df: pandas.DataFrame) -> bool

   Validates if injectionOrder is of integer type.

   :param df: The metadata dataframe.
   :type df: pd.DataFrame

   :returns: Whether the injectionOrder is integer.
   :rtype: bool


.. py:function:: derive_additional_metadata(df: pandas.DataFrame) -> pandas.DataFrame

   Derives additional metadata columns.

   :param df: The metadata dataframe.
   :type df: pd.DataFrame

   :returns: The processed dataframe.
   :rtype: pd.DataFrame


.. py:function:: rearrange_columns(df: pandas.DataFrame) -> pandas.DataFrame

   Rearranges the columns.

   :param df: The metadata dataframe.
   :type df: pd.DataFrame

   :returns: The processed dataframe.
   :rtype: pd.DataFrame


.. py:function:: validate_filenames_column(df: pandas.DataFrame) -> None

   Validates the file names.

   :param df: A dataframe to process.
   :type df: pd.DataFrame

   :raises ValueError: An error if there is any invalid file name.


.. py:function:: add_local_order(file_name: str) -> int

   Returns the localOrder value, i.e. the last n-digits after the last underscore.

   :param file_name: The filename.
   :type file_name: str

   :returns: The localOrder value.
   :rtype: int


.. py:function:: add_sequence_identifier(file_name: str) -> str

   Returns the sequenceIdentifier value, i.e. everything before last _[digits].

   :param file_name: The filename.
   :type file_name: str

   :returns: The sequenceIdentifier value.
   :rtype: str


.. py:function:: separate_filename(file_name: str) -> Tuple[str, str]

   Split a filename into the non-numeric prefix and trailing numeric suffix.

   :param file_name: The filename.
   :type file_name: str

   :returns: Splitted file_name.
   :rtype: Tuple[str, str]


.. py:function:: add_subject_identifier(file_name: str) -> str

   Returns the subjectIdentifier value, i.e. everything between [digit_] and [_digit].

   :param file_name: The filename.
   :type file_name: str

   :returns: The subjectIdentifier value.
   :rtype: str