Example of a MIC Assay Analysis
=============

Collecting the inputs:
*******************

The first step in the analysis of the MIC assay is to collect all variable inputs
.. Link MIC_Input.xlsx template in the repo here
MIC_Input.xlsx consists of multiple sheets

**Substances**

+-----------------------+-------------+-------------+-------------+--------------------+---------------+----------------+
| Dataset               | External ID | Internal ID | Origin Rack | Origin Position 96 | MP Barcode 96 | MP Position 96 |
+=======================+=============+=============+=============+====================+===============+================+
| Cooperation Partner A | 12345       | 1           |             |                    |               |                |
+-----------------------+-------------+-------------+-------------+--------------------+---------------+----------------+

**Organisms**

+-------------------+------+
| Organism          | Rack |
+===================+======+
| Organism A ST1234 | 1    |
+-------------------+------+
| Organism B ST5678 | 2    |
+-------------------+------+
| Organism C ST9101 | 3    |
+-------------------+------+
| ...               | ...  |
+-------------------+------+

**Dilutions**

+---------------+
| Concentration |
+===============+
| 50            |
+---------------+
| 25            |
+---------------+
| 12.5          |
+---------------+
| 6.25          |
+---------------+
| 3,125         |
+---------------+
| 1.56          |
+---------------+
| 0.78          |
+---------------+
| 0.38          |
+---------------+
| 0.2           |
+---------------+
| 0.1           |
+---------------+
| 0.05          |
+---------------+

**Controls**

+------------------+-------------------+----------+
| Dataset          | Internal ID       | Position |
+==================+===================+==========+
| Negative Control | Bacteria + Medium | A23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | C23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | E23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | G23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | I23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | K23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | M23      |
+------------------+-------------------+----------+
| Negative Control | Bacteria + Medium | O23      |
+------------------+-------------------+----------+
| Blank            | Medium            | A24      |
+------------------+-------------------+----------+
| Blank            | Medium            | B24      |
+------------------+-------------------+----------+
| Blank            | Medium            | C24      |
+------------------+-------------------+----------+
| Blank            | Medium            | D24      |
+------------------+-------------------+----------+
| Blank            | Medium            | E24      |
+------------------+-------------------+----------+
| Blank            | Medium            | F24      |
+------------------+-------------------+----------+
| Blank            | Medium            | G24      |
+------------------+-------------------+----------+
| Blank            | Medium            | H24      |
+------------------+-------------------+----------+
| ...              | ...               | ...      |
+------------------+-------------------+----------+
| Reference        | Rifampicin        | N23      |
+------------------+-------------------+----------+
| Reference        | Vancomycin        | P23      |
+------------------+-------------------+----------+

.. code-block:: Python
   :linenos:

   import rda_toolbox as rda

   input_mapping = rda.mic_process_inputs(
       # Input specifications excel:
       "../data/input/MIC_Input.xlsx",
       # Barcode reader file which shows Motherplate to AsT plate mapping
       "../data/input/DiS_MP_AsT_2024-10-08.txt",
       # Barcode reader file which shows Ast plate to AcD plate mapping
       "../data/input/AmA_AsT_AcD_20241009.txt",
   )
   input_mapping.to_csv("../data/processed/prepared_input_mapping_table.csv", index=False)


+----------------+-------------+---------------+-----------------+-------------+---------------+----------------+---------+---------+-----------------+---------------+----------+-----------------+-----------+----------+
| Dataset        | External ID | Original Rack | Origin Position | Internal ID | MP Barcode 96 | MP Position 96 | Row_384 | Col_384 | AsT Barcode 384 | Concentration | Position | AcD Barcode 384 | Replicate | Organism |
+----------------+-------------+---------------+-----------------+-------------+---------------+----------------+---------+---------+-----------------+---------------+----------+-----------------+-----------+----------+
| Coop Partner A | 123456789   | 2233445566    | A1              | 987654321   | 3456677889    | A1             |         |         |                 |               |          |                 |           |          |
+----------------+-------------+---------------+-----------------+-------------+---------------+----------------+---------+---------+-----------------+---------------+----------+-----------------+-----------+----------+
|                |             |               |                 |             |               |                |         |         |                 |               |          |                 |           |          |
+----------------+-------------+---------------+-----------------+-------------+---------------+----------------+---------+---------+-----------------+---------------+----------+-----------------+-----------+----------+

.. code-block:: Python
   :linenos:

   rawfiles = rda.parse_readerfiles("../data/raw/")
   rawfiles.to_csv("../data/processed/rawdata.csv", index=False)

+---------+---------+---------------------+-----------------+
| Row_384 | Col_384 | Raw Optical Density | AcD Barcode 384 |
+---------+---------+---------------------+-----------------+
|         |         |                     |                 |
+---------+---------+---------------------+-----------------+
|         |         |                     |                 |
+---------+---------+---------------------+-----------------+


.. code-block:: Python
   :linenos:

   processed_data = rda.preprocess(
       rawfiles,
       input_mapping,
       substance_id="Internal ID",
       measurement="Optical Density",
       negative_controls="Bacteria + Medium",
       blanks="Medium",
       norm_by_barcode="AcD Barcode 384"
   )