Add helper to convert Bio.Phylo trees to PyTorch #2557
Merged
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
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Outdated suggestions cannot be applied.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.
Addresses #2426
This adds a helper
bio_phylo_to_times()to extract coalescent time statistics from a Bio.Phylo tree object. This is convenient becauseBio.Phyloprovides parsers for most phylogeny tree formats, including Newick and NEXUS. Note this does not add a new dependency to Pyro: the code is duck typed and works wheneverbiopythonis installed (it is not installed by default becausebiopythonrequires Python 3.6+).I plan to document this helper in a new tutorial section #2558. I had already used a version of this helper in previous tutorial sketches.
Tested