BioReport

A package for processing bioinformatics reports.

Current version supports the following report types:

• fastp-json
• fastp-html
• bismark-align
• bismark-deduplicate
• bowtie2-paired
• bowtie2-unpaired

The package is still under development. The framework is designed to be extensible. More report types will be supported in the future.

Install

git clone https://github.com/LawrenceLiu023/bioreport.git
pip install bioreport

Usage

Quick start:

import bioreport
import pandas as pd

# Scan a directory for reports.
report_list = bioreport.scan_dir("/path/to/report/dir")

# Parse all the reports found.
report_sum_list = [r.parse() for r in report_list]

# Combine the parsed reports.
combined_report = bioreport.ReportSum.concat(report_sum_list)

For more details, please see the documentation.