Module chrom 

Chromosome name conversion.

Maps NCBI RefSeq accessions (e.g. "NC_000006.12") to UCSC-style chromosome names (e.g. "chr6"). Patch-sequence accessions (NW_*, NT_*) are returned unchanged so the transcripts on them remain round-trippable, even though they can’t be looked up by standard chromosome name.

This is a hardcoded table for the 25 standard GRCh38 chromosomes. Unknown inputs (anything not in the table and not recognized as a patch accession) are returned as-is.

Functions

is_patch_sequence

Return true if chrom is a non-primary GRCh38 contig — either in the RefSeq accession form (NW_*, NT_* — used by NCBI MANE summary TSVs) or the UCSC alt/fix/random/unlocalized form (used by NCBI MANE GFF3 column 1).

refseq_to_ucsc

Map a RefSeq chromosome accession to a UCSC-style name.

ucsc_to_refseq

Map a UCSC-style chromosome name to a RefSeq accession.