docs

cdot documentation

Reference and how-to docs for cdot. These live in the repo, versioned with the code.

Getting started

• Using local downloaded JSON.gz files - load release files into the HGVS libraries.
• Biocommons HGVS examples - c→g / g→c, plus a T2T-CHM13v2.0 example.
• PyHGVS examples - legacy PyHGVS integration (prefer biocommons).
• FastaSeqFetcher - local FASTA sequence fetching (SeqRepo replacement).

Advanced usage

• Advanced usage - fixing messy HGVS input (fix_hgvs / clean_hgvs) and read-ahead batch retrieval for bulk processing (RESTDataProvider.prefetch).
• Transcript-version safety - the opt-in safe version fallback: how cdot decides a version substitution is coordinate-preserving (is_version_substitution_safe), and the study behind it.

Data format reference

• JSON data format - every field in a cdot JSON(.gz) file, auto-generated from the typed models in cdot/models.py. Machine-readable JSON Schema alongside it.
• Coordinates & exon alignments - how exon coordinates, exon IDs and the alignment gap (CIGAR-like) strings work, with worked examples.

Data files & generation

• GitHub release file details - what each released .json.gz file contains.
• Create data from scratch - build the JSON files yourself from GTF/GFF3.

Background

• cdot vs UTA - how cdot compares to the Universal Transcript Archive.
• Design notes & project direction - why JSON, known issues, project goals.