antigenomics

Extract TCR:pMHC specificity data from raw source files (papers, supplementary tables, XLS, PDF, 10X output, AIRR-format) and produce a VDJdb-formatted TSV chunk ready for /format and /proofread.

Standardise a raw or partially-formatted VDJdb TSV chunk — normalising species names, IMGT V/D/J gene IDs, IMGT-HLA MHC alleles, and method vocabulary — and produce a properly-named chunk file ready for proofreading.

For each new or changed chunk in chunks/ (by git), find or create a GitHub issue for its PMID, then commit the chunk with "Fixes #issue_id". Processes one chunk at a time, always asking user before creating issues or committing.