proteometer.residue
===================

.. py:module:: proteometer.residue


Functions
---------

.. autoapisummary::

   proteometer.residue.get_res_names
   proteometer.residue.get_res_pos
   proteometer.residue.count_site_number
   proteometer.residue.count_site_number_with_global_proteomics


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

.. py:function:: get_res_names(residues: collections.abc.Iterable[str]) -> list[list[str]]

   Extracts residue names from an iterable of residue strings.

   :param residues: An iterable of residue strings, each containing
                    an uppercase letter followed by digits and optional lowercase letters or hyphens.
   :type residues: Iterable[str]

   :returns:

             A list of lists, where each inner list contains the extracted
                 residue names from the corresponding input string.
   :rtype: list[list[str]]


.. py:function:: get_res_pos(residues: collections.abc.Iterable[str]) -> list[list[int]]

   Extracts residue positions from an iterable of residue strings.

   :param residues: An iterable of residue strings, each containing
                    an uppercase letter followed by digits and optional lowercase letters or hyphens.
   :type residues: Iterable[str]

   :returns:

             A list of lists, where each inner list contains the extracted
                 residue positions from the corresponding input string.
   :rtype: list[list[int]]


.. py:function:: count_site_number(df: pandas.DataFrame, uniprot_col: str, site_number_col: str = 'site_number') -> pandas.DataFrame

   Counts the number of sites per protein in a given DataFrame.

   :param df: DataFrame containing protein and site information.
   :type df: pd.DataFrame
   :param uniprot_col: Column name of the protein identifier.
   :type uniprot_col: str
   :param site_number_col: Name of the column to store the site number.
                           Defaults to 'site_number'.
   :type site_number_col: str, optional

   :returns: DataFrame with the site number added.
   :rtype: pd.DataFrame


.. py:function:: count_site_number_with_global_proteomics(df: pandas.DataFrame, uniprot_col: str, id_col: str, site_number_col: str = 'site_number') -> pandas.DataFrame

   Counts the number of sites per protein in a given DataFrame, with the global proteomics
   data used as the reference.

   :param df: DataFrame containing protein and site information. The index of
              this DataFrame must match `id_col`.
   :type df: pd.DataFrame
   :param uniprot_col: Column name of the protein identifier.
   :type uniprot_col: str
   :param id_col: Column name of the identifier that matches the index of the DataFrame.
   :type id_col: str
   :param site_number_col: Name of the column to store the site number.
                           Defaults to 'site_number'.
   :type site_number_col: str, optional

   :returns: DataFrame with the site number added.
   :rtype: pd.DataFrame