Challenge questions

The read_gff() function has an extra argument, extra_attributes, that allows it to extract more attributes than just 'ID' and 'Parent'.

Shouldn't we make our command-line program support this too?

Challenge

Give the gff_to_sqlite program an extra optional argument called 'extra_attributes'. It should be used like this:

In R

Rscript --vanilla gff_to_sqlite.R \
--input my_file.gff \
--output genes.sqlite \
--extra_attributes gene_type gene_name

In python

python gff_to_sqlite.py \
--input my_file.gff \
--output genes.sqlite \
--extra_attributes gene_type gene_name

Connect up this argument so that the attributes appear in the output as well!

Hint. the nargs='+' option to parser$add_argument() can be used to tell argparse that the option should taae one or more values. The values supplied come back as a 'character vector' in R, or

Warning

If you've already created a genes.sqlite database, and you try to re-run the program adding extra columns - it will fail. This is because it's trying to put new columns like gene_type into a table that doesn't have them. Use a new database file or delete the old one instead.