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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
  1. Keep the files in ref_db folder
  2. 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.