GENE TO PATHWAY CONVERTER FOR MASTRO

Install dependencies

pip isntall -r requirements.txt

How to run

To run the converter script run_converter.py, use the following command: ``` usage: run_converter.py [-h] [-i I]

options: -h, --help show this help message and exit -i I Input file ``` The -i parameter specifies the file to convert.

Input

The input file must be formatted like a MASTRO input file. For more information, please refer to the MASTRO documentation.

Output

Running this script will produce several converted files, depending on the number of converters available in the converter/ folder. Each converter generates a separate output file, all of which are stored in the output/ folder. These files can then be used as individual inputs for MASTRO.

Available conversion types

1. close_to_root_converter.py:
2. Description: This conversion method considers nodes that appear closer to the root node of the tree as more important.
3. rnd_int_node_converter.py:
4. Description: This conversion method considers any internal node as important, regardless of its position relative to the root.

How to handle more genes and pathways

When multiple trees with unknown genes are used as input for conversion, it is crucial to provide the gene-to-pathway mapping in the table_gene_path.csv file located in the data/ directory. If you wish to abbreviate the names of these pathways, you must also update the pathways.csv file, which is also found in the data/ directory.

How to add more converter

To add more converter just create a new update_score() function with some criterio to update genes score. Then with the new score system, change the pathwat importance criterio part. For example, in close_to_root_converter.py the criterio check the node with minimum ancestor and if differents nodes have same ancestor, check the which one has maximum descentant.

Analysis.py

This script allows you to analyze the results of various conversions in comparison to the original representation. It is important to run MASTRO on the converted datasets before performing this analysis.

Input

Once all the data has been obtained, you can proceed with the pre- and post-conversion data analysis. In the analysis/ folder, you can run the analysis using the command: ``` usage: trees_analysis.py [-h] [-i I]

options: -h, --help show this help message and exit -i I input file with graphs ``` The following analyses will be performed: - Distribution analysis of tree nodes - Distribution analysis of tree depths - Comparison of the number of patterns found before and after conversion - Comparison of the average trajectories observed from MASTRO analyses before and after conversion

Output

The output will include three files: - Histogram of node distribution - Histogram of tree depths - Table containing the number of patterns and the average trajectories