tecan-od-analyzer 0.1.6
OD data handling for growth curve estimation and visualization of TECAN OD readings
License: MIT

## Description


tecan_od_analyzer is a Python package for analysing optical density (OD) measurements taken from the Tecan Nano plate reader. 

The tool parses the individual xlsx files from the plate reader and merges them into a single xlsx file using the autoflow_parse library. The merged file is read as a dataframe and every sample is labelled according to the calc.tsv file, 
provided by the user. The labelling helps to differentiate the sample purpose, indeed, some samples correspond to growth rate estimation and plotting while others are used to estimate the volume loss.

Once the samples are labelled according to the experiment, the volume loss throughout the culture is estimated and its effect is neutralized using a simple regression model. The next step concerns the outlier detection and growth phase estimation, which are done by using the croissance package. Subsequently, growth rate plots and summary statistics are also computed. The library also provides the functionality of interpolating OD measurements on processed samples at any given time.

### Documentation 

Additional documentation can be found following this url link : https://autoflow-htc.readthedocs.io/en/latest/


## Installation

### Installation using pip 

``pip install tecan_od_analyzer``

### Installation from GitHub using pip

``pip install git+https://github.com/biosustain/AutoFlow-HTC``


## Usage 


tecan_od_analyzer can be used from the command-line by executing it in the directory where the xlsx files are located. The outputs will be gathered on a new directory called "results".

### Command line usage

#### Standard usage :

``tecan_od_analyzer``

The default command produces growth phase estimation, summary statistics on the estimations and growth rate plots split only by species. By default the volumess loss correction is computed.

##### Options :

``tecan_od_analyzer --resultsdir RESULTSDIR`` specifies where the result will be redirected can be a directory name or a path.

``tecan_od_analyzer --path PATH`` specifies where the data is, without the option the program runs in the path where it is executed.

``tecan_od_analyzer --estimations``     Outputs only estimations for every sample in a text file.

``tecan_od_analyzer --figures``         Outputs only the growth curves.

``tecan_od_analyzer --summary``         Outputs only the estimations for every species and bioshaker as well as boxplots of the growth rare annotation parameters.

``tecan_od_analyzer --individual``      Outputs the growth curves for every sample individually.

``tecan_od_analyzer --bioshaker``       Splits the visualization of the growth rate plots according to the bioshaker and species.

``tecan_od_analyser --bioshakercolor``  Splits the visualization of the growth rate plots according to species and colors by bioshaker.

``tecan_od_analyser --interpolationplot``  Outputs Growth rate curves instead of scatter plots.

``tecan_od_analyser --interpolation``   Computes interpolation of samples given the measure time and outputs an xlsx file with the estimations.

``tecan_od_analyser --volumeloss``      This option allows the user to not compute the volume loss correction. By default, the volume loss correction is always computed.


## Input

### Standard required input 


In order to run the program the user has to execute it where the data is. The inputs to the program correspond to the ones required for the autoflow_parser (log file, xlsx file, etc). 

Furthermore, to classify the samples, a file where the purpose of each sample figures is needed. This file must be a tab-separated file (.tsv) with the following format :


| Sample_ID | gr_calc | vl_calc | Species      | Drop_out | Dilution |
|-----------|---------|---------|--------------|----------|----------|
| BS1.A1    | TRUE    | FALSE   | <species_id1> | TRUE     | float  |
| BS1.A2    | FALSE   | TRUE    | <species_id2>          | FALSE    | float |
| ...       | ...     | ...     | ...          | ...      | ...      |


It is important that the headers of every column must be written as it can be seen in the table. Concerning the Sample_ID, the bioshaker must appear at the beggining of the string.

### OD interpolation required input 

To compute the estimations the user must provide a tsv file named as ``od_measurements.tsv`` with the following format :

| Sample_ID           | Time | Regression_used | 
|---------------------|------|-----------------|
| BS1.A1_<species_id> | 0.9  | well            |
| BS1.A2_<species_id> | 0.02 | mean            |
| ...                 | ...  | ...             |

For the regression column, two options are possible. On the first hand, the ``well``option corresponds to interpolate a given OD using only the data of the corresponding well/sample. On the second hand, the ``mean``option computes the interpolation using all the samples that share the same species and bioshaker.

It's relevant to remark, that the numbers appearing in the time column must be written with dots and not with commas. The unit for the time column corresponds to hours. The sample_ID must be followed by the species ID.

## Plotting options

The plots can be customized by selecting how to group the samples and combine them on a single plot. By default, the generated plot will contain all the samples within the same species in one plot. The plots can also be generated separately and split or color labelled by bioshaker.


The different options can be consulted by typing : ``tecan_od_analyzer --help`` or ``tecan_od_analyzer -h``

## Results

It must be noted that all the time units will appear in hours. The Results directory contains an example of the data obtained by running the program with the following command : ``tecan_od_analyzer -bc``

### Figures : 

- Plot of volume loss correlation against the time. ``lm_volume_loss.png``

- Growth rate measurements according to the specified options. The name will change depending on the plotting option. It usually contains the sample ID and the bioshaker.

- Boxplots of the linear phase parameters for splitted by species and bioshakers. Some of the parameters are the intercept, the beggining and end of the linear phase, slope, etc.


### Estimations / Linear phase estimations:

- Linear phase annotations `` annotations.xlsx`` file containing the linear phase estimated parameters for all samples.
- errors.txt  file containing the list of samples for which the linear phase estimation resulted in an error.
- Data_series.xlsx   file containing all the data points after dilution and volume loss correction. The outliers have also been removed.


### Summary statistics:

- summary_stats.xlsx file containing summary statistics of the estimated parameters grouping by species, by bioshaker and both.

## Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

## License

MIT