Small fixes to database pruning and updating

[nickjcroucher]

• Fix to --remove-samples, which did not work due to missing parentheses
• Updated QC mode to also prune samples out of the graph with prune_graph - e.g. for trimming a database, or for removing inappropriate samples only identified after visualisation (I assume networks code will be optimised in the future, so this is a little rough and ready)
• Updated unwords.py to no longer use sets - https://stackoverflow.com/questions/15837729/random-choice-from-set

[johnlees]

I'll have a look at this next week. We also need to co-ordinate with #322 which I had almost finished to fix the latter issue too, maybe I can just remove it from there.

Also, was #304 supposed to have been merged at some point, or does this replace that?

[nickjcroucher]

Apologies, hadn't seen #322 - I don't get notifications of issues as I used to for some reason. These were just the changes I needed to make to prepare data for @absternator. #304 is more a rumination on the nature of time and mortality at this point, but I'll pull across the changes from master into it when I get a chance.

[johnlees]

Check this one against #322 – I think I remember changing it there perhaps. Might be best just to remove this change for now

[nickjcroucher]

I don't think it changes the behaviour if there is no reference file, as in the current GPS database - I suppose it just depends what we want the behaviour to be in such a situation.

[johnlees]

Why this change in behaviour? This would change some of the examples I think

[nickjcroucher]

This harmonises the behaviour of BGMM and DBSCAN - identifying the between-strain cluster as that containing the largest number of points. Name is a bit ugly.

[johnlees]

Where is this now used? Also which distance, as in up or down the y-axis?

[nickjcroucher]

Used in

PopPUNK/PopPUNK/refine.py

Line 117 in 77537af

x_max_start, y_max_start = decisionBoundary(mean0, gradient, adj = -1*min_move)

to harmonise behaviour of unconstrained with other refinement modes.

[nickjcroucher]

Better definition in 2054e6c.

[nickjcroucher]

Thank you for the comments @johnlees! I think I've addressed most of them - would it now make sense:

• merge in this and unword consonants as list #322
• set up an issue for updating the network functions, as suggested here, and to enable GPU-based fast pruning (yes, the can would be kicked down the road)
• set up a new branch to test whether we can get beebop running on the full database using the modifications you suggested, so we can keep @absternator busy?

[johnlees]

One final response in my comments, just on checking input is sorted

Thank you for the comments @johnlees! I think I've addressed most of them - would it now make sense:

* merge in this and [unword consonants as list #322](https://github.com/bacpop/PopPUNK/pull/322)

Let's merge this first. I still wanted to test a couple of things on that branch (should have time in a couple of weeks), then I can just resolve and merge problems on that one myself when it's ready.

* set up an issue for updating the network functions, as suggested here, and to enable GPU-based fast pruning (yes, the can would be kicked down the road)

Yep, good plan

* set up a new branch to test whether we can get beebop running on the full database using the modifications you suggested, so we can keep @absternator busy?

Also makes sense!