vdjdb-format

What problem does it solve?

This skill normalizes and standardizes VDJdb TSV chunks, ensuring compatibility and consistency with the VDJdb and IMGT specifications, reducing the time spent on data validation and formatting.

Core Features & Use Cases

• Standardization of VDJdb Data: Ensures consistency of species names, IMGT V/D/J gene IDs, and MHC alleles according to VDJdb specifications.
• Species Normalization: Automatically corrects and standardizes species names to their VDJdb-accepted format.
• IMGT Gene ID Conversions: Converts IMGT V/D/J gene IDs from various formats to the standardized IMGT notation.
• MHC Allele Standardization: Formats and validates human and mouse MHC alleles to VDJdb/IMGT standards.
• Method Vocabulary Normalization: Transforms method terms used in TSV chunks into recognized VDJdb/IMGT vocabulary.
• Chunk ID Renumbering: Sequentially renumbers chunk IDs after standardization.
• Format Log Generation: Provides a detailed log of changes, discrepancies, and decisions made during standardization.
• Output Filename Specification: Determines output filenames based on publication IDs, alternative identifiers, or submission data.

Quick Start

Execute the 'vdjdb-format /format path/to/chunk_file.tsv' command to standardize the TSV chunk.