vatj/gpmap_integer_polyomino

Code repository for the analysis of the Genotype-Phenotype Map Properties of the Integer Polyomino Model.

gpmap_integer_polyomino's Issues

Genotype/Assembly graph feature identification

What

ID genotype features like

• free faces
• total number of interactions
• assembly graph features
  • branching points
  • cycles
  • SIFs

Why

Better understand phenotype space in general, and specifically how duplication effects different subunits.

How

reconstruct info based on the reference genotype present in set metric file

Packing error

Does graph_topo need to be additionally added to local directory?

If we make a pypi package, it should be 1 click installable, not require many steps.

Clarify "quickstart"

It is confusing to install and use this repo from scratch.

• clarify state system requirements (CMake etc.)
• improve usage of quickstart files
  • remove clutter (privateSainsburyPresentation etc.)
  • comment more on user interface side
  • command line option?
• docs and tests folders are basically nonfunctional

Consistent duplicate generation

What

Duplicates should be taken from the same list that generated the 3 tile space

Why

Removes confusion over parentless duplicates and childless 3 tiles.

How

Save 3 tile list to file, read file, duplicate based on given list
(do we want to strip isomorphic duplicates, it is meaningful that they are twice as common...)