Question about the coordinate systems in use

[ccwang002]

Thanks for developing the genomic tool stack in python. As a user from R/Bioconductor ecosystem, I would like to get some clarifications on the coordinate system in use.

Here is the current description about the coordinate system from BiocPy's documentation

An IRanges holds a start position and a width, and is most typically used to represent coordinates along some genomic sequence. The interpretation of the start position depends on the application; for sequences, the start is usually a 1-based position, ...

>>> from iranges import IRanges
>>> starts = [-2, 6, 9, -4, 1, 0, -6, 10]
>>> widths = [5, 0, 6, 1, 4, 3, 2, 3]
>>> ir = IRanges(starts, widths)
>>> print(ir)
IRanges object with 8 ranges and 0 metadata columns
               start              end            width
    <ndarray[int32]> <ndarray[int32]> <ndarray[int32]>
[0]               -2                3                5
[1]                6                6                0
[2]                9               15                6
[3]               -4               -3                1
[4]                1                5                4
[5]                0                3                3
[6]               -6               -4                2
[7]               10               13                3

This seems to indicate that the BiocPy's coordinate system is 1-based and half open interval, e.g. [start, end).

However, this behavior is different to R's IRanges, where the coordinate system uses a 1-based closed interval, e.g. [start, end]:

> library(IRanges)
> starts = c(-2, 6, 9, -4, 1, 0, -6, 10)
> width = c(5, 0, 6, 1, 4, 3, 2, 3)
> ir <- IRanges(start = starts, width=width)
> ir
IRanges object with 8 ranges and 0 metadata columns:
          start       end     width
      <integer> <integer> <integer>
  [1]        -2         2         5
  [2]         6         5         0
  [3]         9        14         6
  [4]        -4        -4         1
  [5]         1         4         4
  [6]         0         2         3
  [7]        -6        -5         2
  [8]        10        12         3

Wanted to clarify if the design is intentional. If so, could we note the different behaviors between BiocPy's and R's IRanges in the documentation? I was wondering if we could also create some utility functions to convert across the coordinate systems, so it's easy to port the existing R scripts that expects a 1-based closed interval.

Thank you again for making the tool!

[jkanche]

Hi, Thank you for reporting this. My best guess is, this is mostly related to how we compute the ends (start + width, start + width -1), we should subtract 1 base to keep the intervals closed and conform to R's IRanges. I'll also perform some tests to make sure thats the case with the methods as well.