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add_pbs #2777

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add_pbs #2777

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atongsa
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@atongsa atongsa commented Jul 6, 2023

Description

sorry i messed and delete my local branch, so the pr #2749 was closed automately;
i don't know how to reopen, so i opened a new pr;
sorry agian;

Closes #2717

PR Checklist:

  • Tests that fully cover new/changed functionality.
  • Documentation including tutorial content if appropriate.
  • Changelogs, if there are API changes.

@atongsa atongsa changed the title 20230706_pbs add_pbs Jul 6, 2023
@petrelharp petrelharp mentioned this pull request Jul 6, 2023
divergences.shape = (divergences.shape[0], 1, divergences.shape[1])
diversities.shape = (diversities.shape[0], 1, diversities.shape[1])

fst = np.repeat(1.0, np.product(divergences.shape))
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I think it would be better just to call self.Fst( ) directly instead of copying the code.

)
fst.shape = orig_shape

def cal_pbs(arr_0):
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I don't think we're gaining anything by separating this out into a function that is immediately called.


"""

def pbs_func(sample_set_sizes, flattened, indexes], **kwargs):
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stray ]

@petrelharp
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I started commenting on the code, @atongsa, but noticed a bunch of typos, e.g.,

                            2 * (div=ersities[:, :, u] + diversities[:, :, v]) / denom

Please let us know when you've got code that runs (at least, doesn't have syntax errors)? Or, ask if you have specific questions about the approach?

@benjeffery
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Hi @atongsa - are you planning to come back to this work? Thanks!

@atongsa
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atongsa commented Sep 30, 2024

sorry, it is a little difficult for me, i don't understand the errors, and has no idea how to fix it, i need to read more about the funcions and docs.

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Add 'PBS()'
3 participants