edinburgh-genome-foundry / saboteurs Goto Github PK

Consider the following scenario:

id	attempts	failures	members
construct_1	3	3	A	B	C	D
construct_2	3	0	E	C	D	
construct_3	3	0	A	B	F	

The problem here is that certain member-combinations fail the assembly (mission), but that cannot be inferred with either methods.
statistical_assembly_data.csv

A related issue: in DNA assembly the above can be explained by that each part (member) has 2 ends (overhangs) that join with other parts; if A=1&2, B=2&3 and so on, then we can rewrite the table with overhangs:

id	attempts	failures	members				
construct_1	3	3	1	2	3	4	0
construct_2	3	0	1	3	4	0	
construct_3	3	0	1	2	3	0	

Then it's clear that interaction (misannealing) between 2 and 4 causes the problem.

This is outside scope of the package, but can be a good Example.
statistical_assembly_data_overhangs.csv