parse_module_definitions
========================

.. py:module:: parse_module_definitions

.. autoapi-nested-parse::

   author: Haris Zafeiropoulos
   package: microbetag
   description: Aim of this script is to build all the unique sets of KO terms that can be used to build up each KEGG module (https://www.genome.jp/brite/ko00002)
   output: A 2-levels .json file, in the first one, the various steps will be denoted and in the second the multiple alternative combinations of terms
           will be shown. All the terms of a combination are necessary for the module to be complete
   notes: The pathway module is defined by the logical expression of K numbers, and the signature module
           is defined by the logical expression of K numbers and M numbers.
           A SPACE ( ) or a PLUS (+) sign, representing a connection in the pathway or the molecular complex, is treated as an AND operator
           and a COMMA (,), used for alternatives, is treated as an OR operator.
           A MINUS (-) sign designates an optional item in the complex.
           This script was inspired by 2 functiosn from the following script of microbeAnnotator:
           https://github.com/cruizperez/MicrobeAnnotator/tree/master/microbeannotator/data/01.KEGG_DB/00.KEGG_Data_Scrapper.py



Attributes
----------

.. autoapisummary::

   parse_module_definitions.structurals
   parse_module_definitions.modules
   parse_module_definitions.module_components_raw
   parse_module_definitions.definition
   parse_module_definitions.module_steps_parsed
   parse_module_definitions.P
   parse_module_definitions.q
   parse_module_definitions.module


Functions
---------

.. autoapisummary::

   parse_module_definitions.flatten
   parse_module_definitions.parse_commas_on_pre_and_post_character
   parse_module_definitions.check_if_all_in_one_par
   parse_module_definitions.get_independent_step_alternatives
   parse_module_definitions.split_to_independent_chunks
   parse_module_definitions.parse
   parse_module_definitions.parse_regular_module_dictionary
   parse_module_definitions.create_final_regular_dictionary


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

.. py:data:: structurals
   :value: ['M00144', 'M00149', 'M00151', 'M00152', 'M00154', 'M00155', 'M00153', 'M00156', 'M00158', 'M00160']


.. py:function:: flatten(lis)

   Takes a nested list and returns its contents in a sequential one
   e.g. [[a,b,c,][d,e,]] --> [a,b,c,d,e]


.. py:function:: parse_commas_on_pre_and_post_character(string)

   Takes a string and returns independent scenarions separated by commas (,)
   e.g. K02304,(K24866+K03794)
   ['K02304', '(K24866+K03794)']


.. py:function:: check_if_all_in_one_par(string)

   Function to tell you whether a string is included in a single parenthesis
   e.g.:  ((K00705,K22451)_(K02438,K01200))
   or not
   e.g.: K00975_(K00703,K13679,K20812)


.. py:function:: get_independent_step_alternatives(step_as_a_list)

   It takes a complete step and returns its unique indipendent pats recursively
   e.g.:
   in the first round for
   ((K13939,(K13940,K01633 K00950) K00796),(K01633 K13941))
   we get the (K01633 K13941)) as an independent way
   while in the second one, we get the K13939


.. py:function:: split_to_independent_chunks(string)

   Takes a string and returns indices where you can split it to parts that can be combined
   independently to get the part of the corresponding KEGG module definition
   e.g. "K00941_(K00788,K21220)"
   [0, 7, 22]
   or
   "((K03831,K03638)_K03750)"
   [0, 24]


.. py:function:: parse(my_string)

   Parses a module's definitions to each main steps
   e.g.
   md definition: (K02303,K13542) (K03394,K13540) K02229 (K05934,K13540,K13541) K05936 K02228 K05895 K00595 K06042 K02224 K02230+K09882+K09883
   ['(K02303,K13542)', '(K03394,K13540)', 'K02229', '(K05934,K13540,K13541)', 'K05936', 'K02228', 'K05895', 'K00595', 'K06042', 'K02224', 'K02230+K09882+K09883']


.. py:function:: parse_regular_module_dictionary(module_components_raw, structural_list)

   Breaks down a module to its steps using the parse() function


.. py:function:: create_final_regular_dictionary(module_steps_parsed)

   This function returns all the possible combinations of KOs to have a complete KEGG module


.. py:data:: modules

.. py:data:: module_components_raw

.. py:data:: definition

.. py:data:: module_steps_parsed

.. py:data:: P

.. py:data:: q

.. py:data:: module