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: fourfinger-analysis.zip (Right click, Save As)