User Guide

User Guide

Command-Line Interface (CLI)

Basic Usage

Process a single file:

phenoqc --input examples/sample_data.csv --output ./reports/ --schema schemas/pheno_schema.json --mapping examples/sample_mapping.json --impute mean

Batch process multiple files:

phenoqc --input data1.csv data2.json data3.tsv --output ./reports/ --schema schemas/pheno_schema.json --mapping examples/sample_mapping.json --impute median

CLI Options

• --input: Input file(s) to process
• --output: Directory to save output reports
• --schema: JSON schema file for validation
• --mapping: Custom mapping file for ontology mapping
• --impute: Strategy for imputing missing data (mean, median)

Graphical User Interface (GUI)

To launch the GUI:

streamlit run src/gui.py

Follow the on-screen instructions to upload files, select options, and generate reports.

Configuration

PhenoQC can be configured using YAML or JSON configuration files. Example:

input_files:
- data1.csv
- data2.json
output_directory: ./reports
schema_file: schemas/pheno_schema.json
mapping_file: examples/sample_mapping.json
imputation_strategy: mean

Save this as config.yaml and use it with the CLI:

phenoqc --config config.yaml

Output

PhenoQC generates the following outputs:

1. QC Report (PDF)
2. Visual Summary (PNG)
3. Processed Data (CSV)

These files will be saved in the specified output directory.