indi_report

This program generates reports (in PDF) for individual patient from the microbiome signatures

Installation and Setup:

List of packages:

The environment has been provided in requirements.txt file. Don't need to install each package separately. However, if any package fails to install, install them explicitly.

• pandas
• numpy
• matplotlib
• seaborn
• scipy
• Pillow
• fpdf2
• openpyxl
• ipykernel

Steps to follow:

1. Install VS Code
2. Install Anaconda
3. Open Anaconda Prompt
4. Navigate to the indi_report folder
5. Run the following commands:

• conda create --name indi_report --file requirements.txt
• conda activate indi_report
• python -m ipykernel install --user --name=indi_report

Setup Reference DB

The tool comes with a default reference DB by including KORA healthy, KORA obese and Student cohort of 2016, 2017, 2018, 2019, 2023. The data is kept in ref_db folder. To update the DB,

1. Execute IMNGS2 / NGSToolkit on the reference samples: KORA-Healthy, KORA-Obese, and Student cohort -> Generate zOTU table
2. Execute Rhea:

• Alpha diverisity: required file alpha-diversity.tab
• Beta diversity on KORA-Healthy and Students cohort: required file samples-Tree.nwk
• Taxonomy binning on KORA-Healthy, KORA-Obese, and Students cohort: required files 1.Phyla.all.tab and 5.Genera.all.tab

3. Keep the files in ref_db folder
4. Modify the clade.tab file to match with the clades in the tree

Execution:

1. Open patientReport_v1.ipynb on VS Code
2. Select indi_report environment on VS Code
3. You are ready to generate reports

Files

• patientReport_v1:
• patientReport_v2: It is able to run Rhea from python. However, not all the computers support this feature.
• functions.py: All the necessary functions are present in the file.