edits for DFE-alpha #119
Closed
edits for DFE-alpha #119
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
andrewkern
reviewed
Jul 30, 2024
silastittes
commented
Jul 30, 2024
workflows/ts2fs.py
Outdated
Comment on lines
365
to
369
| neu_len = round(seq_len * kwargs['neu_prop']) | ||
| neu_fs[0] = neu_len - sum(neu_fs[1:]) | ||
| nonneu_len = round(seq_len * kwargs['nonneu_prop']) | ||
| nonneu_fs[0] = nonneu_len - sum(nonneu_fs[1:]) | ||
|
|
There was a problem hiding this comment.
Need to add something similar in _generate_dfe_alpha_fs. Right now the first bin is ALL positions including mutated and substitutions. This is the right format form some software, but not for DFE-alpha.
silastittes
commented
Jul 30, 2024
silastittes
commented
Jul 30, 2024
Comment on lines
+155
to
+169
| rng = default_rng(42) | ||
| neutral_subs_draw = rng.poisson(total_neutral_subs) | ||
|
|
||
| #add neutral subs to last bin | ||
| mut_afs["neutral"][-1] = neutral_subs_draw | ||
|
|
||
| #add in ancestral counts | ||
| mut_afs["neutral"][0] = neutral_anc_count | ||
| mut_afs["non_neutral"][0] = non_neutral_anc_count | ||
|
|
||
| # Remove mutated sites from first bin | ||
| mut_afs["neutral"][0] = mut_afs["neutral"][0] - sum(mut_afs["neutral"][1:]) | ||
| mut_afs["non_neutral"][0] = mut_afs["non_neutral"][0] - sum(mut_afs["non_neutral"][1:]) | ||
|
|
||
| print(f"AFSs\nNeutral: {mut_afs['neutral']}\nNon-neutral: {mut_afs['non_neutral']}") |
There was a problem hiding this comment.
poisson draw and removing mutations from ancestral monomorphic counts
|
closing because now subset of what's in #120 |
Merged
|
This one has some edits we need. Should be good to merge |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.