pyDIOPT

This is the unofficial, opinionated DIOPT python wrapper for the DIOPT ortholog finder.

Installation

pip install pyDIOPT

Example

A couple examples of how to run the wrapper. The standard output is organized into pd.DataFrame for easier downstream manipulations and whatever you want (or can) do with ortholog data (?).

from pyDIOPT import DIOPTRelease

release = DIOPTRelease("v8", "h sapiens")

# fetching single gene
example1 = release.fetch("ENSG00000085117", target_species=None)

# fetching several genes
example2 = release.fetch(
    ["MDM2", "TP53"], target_species="mouse", filter="best_match", condensed=False
)

Acknowledgement

• This repo is boilerplated from py-package-template

• To retrieve the information on citing the original papers, run

  import pyDIOPT
  pyDIOPT.citation()