feat: Add IO for DistanceMatrix in Phylip format #469
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
This mirrors `newick.rs` and adds string/file IO for the `bio_types::distancematrix::DistanceMatrix` type, in the Phylip distance matrix format. It supports square and (upper/lower) triangular matrices. Triangular matrices must not contain the diagonal. Also fix a broken doctest.
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Outdated suggestions cannot be applied.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.
This mirrors
newick.rsand adds string/file IO for thebio_types::distancematrix::DistanceMatrixtype, in the Phylip distance matrix format.It supports square and (upper/lower) triangular matrices. Triangular matrices must not contain the diagonal.
Currently this is assuming the 'relaxed' format with arbitrary long names and single space separators. The 'strict' format requires names of exactly 10 chars (padded with whitespace) and is less flexible because of this.
I didn't find an actual proper spec for this format, but the closest one is probably this.
Also fix a broken doctest.
This will need to be merged after rust-bio/rust-bio-types#35, and the version of
bio-typesneeds to be bumped.