Add tskit CLI #374
Add tskit CLI #374
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bio2zarr/cli.py
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| @click.command(name="convert") | ||
| @click.argument("ts_path", type=click.Path(exists=True)) | ||
| @click.argument("zarr_path", type=click.Path()) | ||
| @click.option( |
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Let's not bother with ploidy - we only support tskit files that have individuals here. Older files can go through the tskit VCF route, or just add the appropriate individuals.
bio2zarr/cli.py
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| setup_logging(verbose) | ||
| check_overwrite_dir(zarr_path, force) | ||
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| import tskit |
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So, we don't need to bother importing tskit here or specifying the individuals_nodes, we just pass in the ts_path
benjeffery
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Ok, pushed a new commit that makes The CLI code now doesn't need to import tskit and ploidy is removed. |
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Great, let's build on this |
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Ok, tests added and other tests modified for new |
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Need to cover num_individuals == 0 error, good to merge after that |
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Test added |
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Looks like this needs a rebase, we've got a conflict |
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Let's just drop python 39, it's not worth keeping around now. |
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Looks like I lost some changes in the rebase, will fix! |
Here's a sketch of how the tskit CLI could look. I'll add tests once were happy with it.