Add cloning function

[Koeng101]

The following branch "goldengatev1" has a functioning GoldenGate assembly script for BbsI. It works, but we should try to break it before integrating it, as well as debate the merits of my approach. It only operates on raw sequences as well - we should likely have an algorithm that works with Genbank files.

If we decide to do something else, we should close this pull request. This function, however, does work.

[qlty-cloud-legacy]

Code Climate has analyzed commit 1a97dfe and detected 107 issues on this pull request.

Here's the issue category breakdown:

Category	Count
Complexity	1
Bug Risk	6
Style	100

The test coverage on the diff in this pull request is 83.9% (95% is the threshold).

This pull request will bring the total coverage in the repository to 96.0% (-1.0% change).

View more on Code Climate.

[rkrishnasanka]

@Koeng101 I would say that having the function work with raw sequences is the best way to go, You could eventually have layers of abstraction in terms of sequence/parts/io-format later on that call the sequence version of this.

[Koeng101]

@rkrishnasanka I agree!

[TimothyStiles]

@Koeng101 can you comment all exported functions? Code climates bots comments are super annoying to read through when doing code review.

[Koeng101]

To go over limitations:

1. We can only cut with 4 enzymes right now (can easily be expanded with rebase)
2. No enzymes can be added that have a single recognition site but multiple cut sites (those aren't really used often anyway).

[TimothyStiles]

1. We can only cut with 4 enzymes right now (can easily be expanded with rebase)

Can you open a new pull request for this and explain why we aren't adding it yet?

2. No enzymes can be added that have a single recognition site but multiple cut sites (those aren't really used often anyway).

I'm not sure what you mean here. Writing feels unclear.

@Koeng101 is the second limitation documented in the example / code itself?

[Koeng101]

I'm not sure what you mean here. Writing feels unclear.

Type IIG restriction enzymes like BcgI. It has a single recognition site, but multiple cut sites. We cannot yet simulate this. I'll in a specific example into the docs because I think that would help with clarity.

Can you open a new pull request for this and explain why we aren't adding it yet?

Should I just open an issue for this?

[TimothyStiles]

Can you open a new pull request for this and explain why we aren't adding it yet?

Should I just open an issue for this?

Yes, I meant to say issue here my bad!

[jkhales]

🥳