Genomic coordinates

All genomic coordinates inside pybio are 0-based, left+right inclusive. So a range written 100-103 includes coordinates 100, 101, 102 and 103. The first coordinate of any sequence is 0.

Important

RefSeq and Ensembl GTF files are 1-based. When pybio reads annotation from RefSeq or Ensembl, it subtracts 1 from every coordinate so that everything inside pybio — genes, transcripts, exons, UTRs, and the coordinates you pass to seq() and annotate() — stays consistently 0-based.

This matters whenever you compare a position from pybio against one from a 1-based source (a GTF file, a VCF, a genome browser coordinate you typed by hand): subtract 1 from the 1-based position before passing it to pybio, or add 1 back when displaying a pybio position to a user.