R <-> Python transpiler

Dmitrii Borisevich

Python and R are two major programming languages used for research software development and data analysis in bioinformatics. It is not a symbiotic relationship, but a cold war between the fans of both.

Different tools are available to use R in python and vice versa, but they demand learning both languages. This is not easy, and thus rarely adopted.

This talk will pitch an idea of using AST to build a transpiler between two languages and showcase a simple demo of converting code written in one language directly into another.

The talk will present:

• the R vs python problem and its consequences in bioinformatics,
• the idea of a transpiler,
• some examples of existing transpilers,
• a demo of R <-> python PoC transpiler.

Questions and comments

• comment: great point about tools possibly dividing communities

• Links for related software

  • The OneLang demo: https://ide.onelang.io/ (https://github.com/onelang/OneLang)
  • Transfer data frames between python and R: https://blog.rstudio.com/2016/03/29/feather/
  • An Rstudio supported projects for using python code in R with R syntax: https://cran.r-project.org/web/packages/reticulate/vignettes/calling_python.html
  • A non-profit that has been supporting software development in both the PyData stack and R for the last decade: https://numfocus.org/
  • CBioVikings - Danish Comp Bio community - https://twitter.com/CBioVikings, https://www.instagram.com/cbiovikings/

• Q: optimal R programming would likely involve making use of its vectorization capabilities, for example by using apply functions instead of loops. Is this something that rtopython-mapping plans to implement?

  • numpy provides these opportunities, so it is possible, hopefully feasible :-)

• Q: Why the comments cannot be translated? Just currious.

  • this can be done, the PoC uses ASTs (abstract syntax trees) for the conversion, and comments are not a part of AST; but this could have been added on top

• Q: how it works under the hood?

  • AST converter from R to python for the grammar + huge map, implementing the functions from R as python AST structure