CLI option setting up custom

[RemyLau]

Currently, if a user wants to use GenePlexus with their custom network or gsc, they will need to set up the required custom files using the geneplexus.custom module first, before they can proceed to run the GenePlexus pipeline using the CLI.

The goal here is to make a CLI option that calls the necessary geneplexus.custom functions to set up custom files, and thus eliminates the need for one to manually prepare them.

Working notes

• [ ] --custom option -> enables preprocessing custom network/gsc data
  • [ ] Preprocessing runlong also save to ${data_dir}/custom_logs/${net}_${feature}_${gsc}.log
    • Network stats: num_nodes, num_edges
    • GSC stast: num_genesets, med_size, avg_size, std_size, max_size, min_size
• Required files
  • Edgelist_xxx.edg (custom network)
  • GSCOriginal_xxx.json (custom gsc)
• [ ] Set up custom network and gsc
  • custom.edgelist_to_node -> NodeOrder_${net}.txt
  • custom.edgelist_to_matrix -> Data_${feature}_{network}.npy
  • custom.subset_gsc_to_network -> GSC_${gsc}_${net}_GoodSets.json, GSC_${gsc}_${net}_universe.txt