Single Origami Analysis
=======================

The **scaffoldselector** can run Metrics 1, 2, 3 and 4 on a single origami (supplied as contact map) and produce a detailed output report featuring origami statistics, metric scores, metric energy distribution histograms and a graphic of off-target staple-scaffold binding sites. 

1. Place the contact map of the origami to analyse in the ``origami/scaffoldselector/_input`` directory, e.g. ``origami/scaffoldselector/_input/myorigami.csv``.

2. Run: ::
	
	cd origami
	source venv/bin/activate
	cd scaffoldselector
	python3 analysis.py myorigami

The program will generate output similar to the following. Execution time may be up to a few minutes, depending on the size of the origami: ::

	--------------------------

	 SCAFFOLD SELECTOR
	 Single Origami Analysis

	--------------------------

	Origami : fourfinger

	Setting up...
	[Done]
	Loading settings.json...
	[Done]
	Loading origami contact map...
	[Done]
	Pre-computing lookup tables...
	[Done]
	Verifying origami contact map...
	[Success]
	Computing Metric 1 energy distributions and binding site diagram...
	[Done]
	Computing Metric 2 energy distribution...
	[Done]
	Computing Metric 4 energy distribution...
	[Done]
	Computing Metric 3 energy distribution...
	[Done]
	Calculating number of staples with G quadruplex...
	[Done]
	Finding primers for DNA scaffold...
	[Done]
	Producing report...
	[Done]

	Report at:
	--> _results/fourfinger.html

3. Open the HTML report ``origami/scaffoldselector/_results/myorigami.html`` in a web browser.

An example analysis file for a fourfinger origami: :download:`fourfinger-analysis.zip<linked_files/fourfinger-analysis.zip>` (Right click, Save As)