The function, get_region_coordinates, returns the coordinates of the regions after incorporating 5' and 3' UTR junctions. Though sometimes, the users need the original region boundaries.
New proposal is as follows:
Let's keep the function get_region_coordinates as is for back-compatibility reasons.
Let's introduce a function called get_internal_region_coordinates that provides the exact functionality of get_region_coordinates. We can provide and encourage this in the documentation of the coming version / release.
Let's implement a function called get_original_coordinates that provides the annotated coordinates of the regions. By annotated, we mean the coordinates coming from the originally curated annotation (from GENCODE, UCSC, etc.) where CDS region starts with the start codon ATG.
The function, get_region_coordinates, returns the coordinates of the regions after incorporating 5' and 3' UTR junctions. Though sometimes, the users need the original region boundaries.
New proposal is as follows:
get_region_coordinatesas is for back-compatibility reasons.get_internal_region_coordinatesthat provides the exact functionality ofget_region_coordinates. We can provide and encourage this in the documentation of the coming version / release.get_original_coordinatesthat provides the annotated coordinates of the regions. By annotated, we mean the coordinates coming from the originally curated annotation (from GENCODE, UCSC, etc.) where CDS region starts with the start codon ATG.