https://github.com/tskit-dev/tsconvert
Utilities for converting tree sequences to and from other formats
https://github.com/tskit-dev/tsconvert
Last synced: 3 months ago
JSON representation
Utilities for converting tree sequences to and from other formats
- Host: GitHub
- URL: https://github.com/tskit-dev/tsconvert
- Owner: tskit-dev
- License: mit
- Created: 2019-01-17T14:39:06.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2025-03-19T13:54:34.000Z (about 1 year ago)
- Last Synced: 2025-03-19T14:25:54.119Z (about 1 year ago)
- Language: Python
- Size: 66.4 KB
- Stars: 7
- Watchers: 5
- Forks: 6
- Open Issues: 21
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# tsconvert
Utilities for converting [tskit](https://github.com/tskit-dev/tskit) tree sequences to
and from other formats.
`tsconvert` is in early development
## Roadmap for v0.1
- Where conversion methods are widely used and do not require any dependencies,
they will be implemented in `tskit`, for example writing VCF. `tsconvert` can then call
the `tskit` method so that it has a complete list. Methods that require dependancies
will be implemented here to avoid dependency bloat in `tskit`.
- Provide either `to_`, `from_` (or both as appropriate) methods
for the following formats:
- [ ] vcf
- [ ] ms
- [ ] argon
- [ ] newick
- [ ] newick + csv/tsv metadata
- [ ] nexus
- [ ] sgkit
- Where a format doesn't provide a full tree sequence it will
have a `parse_` method:
- [ ] plink (pedigree)
- Allow these methods to be used from the CLI, including streams.