Python rewrite of William Engels's Amplify4 by two people who went to Pembroke College Cambridge, hence AmplifyP.
This is pretty much a work in progress.
These are all notes for Fufu to understand.
A replication configuration (Repliconf) consists of a long strand of DNA which acts as the template, and a primer.
The search() function enumerates all the possible replication origins, and calculate the primability and stability score. For a potential replication origin, if the primability and stability scores are above the threshold, the index (location) of this potential replication origin is considered as valid. It is recorded in origin_idx.fwd and origin_idx.rev. Note that during the search, the template sequence is searched in both forward and reverse direction. The process of search in the reverse direction involves reversing the DNA template. (I will add more information about the reverse compliment later.)
Please invoke pytest at the root of the repository.