Taking the easy way

The simplest way to make a 'package' is to just put our function into a single file, like this:

In R

Copy and paste the function and paste it into a new file, called gff.R, in the current directory. (For good measure, paste the test function as well.)

To load this into your R session, you can use the source() function:

source( 'gff.R' )
X = read_gff( "gencode.v41.annotation.head.gff" )

In python

Making a python module is easy:

• Copy your code into a new file, named gmsgff.py using a text editor. (This file should go in your current directory i.e. the one you started python / jupyterhub from.)

• Congratulations! You have now written your first python module.

To use your python module, simply import it and use like this:

import gmsgff
X = gmsgff.read_gff( 'gencode.v41.annotation.head.gff' )

or

X = gmsgff.read_gff( 'gencode.v41.annotation.head.gff', extra_attributes = [ 'gene_type', 'gene_name' ] )

or if you don't want to type the "gmsgff." before the function name:

from gmsgff import read_gff
X = read_gff( 'gencode.v41.annotation.head.gff' )

Cool!

For python this is it!

However, if you're working in R, this isn't a fully-fledged package yet. For that, go here.