proteometer.ptm
===============

.. py:module:: proteometer.ptm


Functions
---------

.. autoapisummary::

   proteometer.ptm.get_ptm_pos_in_pept
   proteometer.ptm.get_yst
   proteometer.ptm.get_phosphositeplus_pos
   proteometer.ptm.combine_multi_ptms


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

.. py:function:: get_ptm_pos_in_pept(peptide: str, ptm_label: str = '*', special_chars: str = '.]+-=@_!#$%^&*()<>?/\\|}{~:[') -> list[int]

   Get the positions of PTM labels in a peptide.

   This function processes a peptide string to find the positions of
   post-translational modification (PTM) labels. It accounts for special
   characters and returns a list of positions adjusted to the stripped
   peptide sequence. Positions are 0-indexed from the start of the peptide.

   :param peptide: The peptide string potentially containing PTM labels.
   :type peptide: str
   :param ptm_label: The label representing PTM. Defaults to '*'.
   :type ptm_label: str, optional
   :param special_chars: A string of special characters that
                         might need escaping in regex operations. Defaults to common
                         special characters.
   :type special_chars: str, optional

   :returns:

             A sorted list of integer positions where the PTM labels
                 occur in the peptide, adjusted for any modifications made during
                 processing.
   :rtype: list[int]


.. py:function:: get_yst(strip_pept: str, ptm_aa: str = 'YSTyst') -> list[tuple[int, str]]

   Get YST positions in a peptide.

   This function takes a stripped peptide sequence and finds the positions of
   Y, S, and T residues.

   :param strip_pept: The stripped peptide sequence.
   :type strip_pept: str
   :param ptm_aa: The residues letters for Y, S, and T residues. Defaults to 'YSTyst'.
   :type ptm_aa: str, optional

   :returns:

             A list of tuples where the first element is the
                 position of the label in the stripped peptide and the second
                 element is the YST residue letter.
   :rtype: list[tuple[int, str]]


.. py:function:: get_phosphositeplus_pos(mod_rsd: str) -> list[int]

   Extracts numeric positions from a string of modified residues.

   :param mod_rsd: A string of modified residues.
   :type mod_rsd: str

   :returns: A list of numeric positions extracted from the input string.
   :rtype: list[int]


.. py:function:: combine_multi_ptms(multi_proteomics: dict[str, pandas.DataFrame], par: proteometer.params.Params) -> pandas.DataFrame

   Combines multiple proteomics dataframes into a single dataframe.

   This function processes and combines different types of proteomics
   data into a unified dataframe. It distinguishes between global
   proteomics data and post-translational modifications (PTM) data,
   assigning specific labels and counting site numbers accordingly.

   :param multi_proteomics: Dictionary of proteomics dataframes
                            with keys indicating the type of proteomics ('global' or PTM types).
   :type multi_proteomics: dict[str, pd.DataFrame]
   :param par: Configuration parameters containing column names and PTM details.
   :type par: Params

   :returns:

             A combined dataframe containing all the input proteomics data,
                 labeled and processed as per the specified parameters.
   :rtype: pd.DataFrame