Output number of nodes per subtree

[Haddox]

@willdumm: @jgallowa07 and I were thinking it'd be nice to have your script output the number of nodes per subtree. Would it be possible to include this in the founder_muts output dataframe by adding a new column that gives number of nodes associated with each founder's subtree? Thanks!

[Haddox]

Then @jgallowa07 would be great to plot the distribution of this metric.

[willdumm]

Since a single node may be the founder for multiple subtrees in different windows, I'll change the founder_muts data frame to contain exactly one entry per subtree, with window start time, subtree size, founder node id, and founder muts.

[willdumm]

@jgallowa07 this is committed in the wd-add-subtree-size branch, but I'm not quite sure how to test -- just the commands in the readme?

[Haddox]

@jgallowa07: in the current version of the founder_muts dataframe, each unique founder sequence has one row. The update in this branch may result in some founders having multiple unique rows if they are founders in multiple unique windows. Do you think this would affect the pipeline you've put together so far?

[jgallowa07]

Sorry for getting to this so late:

Since a single node may be the founder for multiple subtrees in different windows, I'll change the founder_muts data frame to contain exactly one entry per subtree, with window start time, subtree size, founder node id, and founder muts.

@willdumm Nice!

this is committed in the wd-add-subtree-size branch, but I'm not quite sure how to test -- just the commands in the readme?

@willdumm Did you test that it works locally/outside the pipeline? If so that's totally fine by me - I'll test it in the context of the pipeline.

in the current version of the founder_muts dataframe, each unique founder sequence has one row. The update in this branch may result in some founders having multiple unique rows if they are founders in multiple unique windows. Do you think this would affect the pipeline you've put together so far?

@Haddox Nope the pipeline so far only outputs will's output - I'll just keep this in mind for the expected observed counts step that's currently being worked on and change it accordingly once I integrate / run this change through the pipeline.

[jgallowa07]

@willdumm - I incorporated your changes in e6ea2a7 It seems to work as expected, thanks a ton! I'll close this once I take a closer look and get the expected counts algo finished.