Foundation Medicine Parser

Foundation Medicine is a company that provides comprehensive genomic profiling services for cancer patients. The Foundation Medicine Parser is a Python package that allows users to parse the Foundation Medicine reports and extract the relevant information. The package is designed to work with the Foundation Medicine reports in XML format.

Installation

The Foundation Medicine Parser can be installed using pip:

pip install https://github.com/seandavi/foundation-medicine-xml-parser.git

Usage

While the library can be useful by itself, the main entry point for most users will be the process_fmi command line utility. This utility will parse the Foundation Medicine XML files in a directory and output the results of the parsing to an Excel file and a set of CSV files.

process_fmi --input_dir /path/to/foundation-medicine-xml-files --output_dir /path/to/output

The output directory will contain (currently) these files:

output_dir
├── assay_and_patient_data.csv
├── biomarkers.csv
├── copy_number_alterations.csv
├── fmi_report.xlsx
├── rearrangements.csv
└── short_variants.csv

The CSV files contain the parsed data in a tabular format. The Excel file contains the same data in separate worksheets.