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Add DATA block to as_nexus #1840

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jeromekelleher opened this issue Oct 25, 2021 · 1 comment
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Add DATA block to as_nexus #1840

jeromekelleher opened this issue Oct 25, 2021 · 1 comment
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@jeromekelleher
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#1838 updated the as_nexus method to make it more standards compliant. Before we release this in 0.4.0 we should (at least) decide whether we should include the alignments in the DATA block of the nexus file. (Like this example)

Since the as_nexus/write_nexus methods are new in 0.4.0 I guess we should either (a) output alignments in the DATA block or (b) document that we want to do this later and that the default will always be to not output the alignments. However, once we have #1825 merged it should be pretty straightforward to implement. I presume things like matchchar are optional?

@jeetsukumaran any thoughts here? Would it be expected that a nexus conversion should output the full data set by default, or just include the trees?

@jeetsukumaran
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I think would expect the entire dataset to be written out unless I specified otherwise (e.g., is_include_chars=False or is_exclude_chars=True, depending on which idiom you like, along with a parallel is_include_trees/is_exclude_trees).

@jeromekelleher jeromekelleher added this to the Python 0.4.0 milestone Oct 25, 2021
jeromekelleher added a commit to jeromekelleher/tskit that referenced this issue Nov 7, 2021
jeromekelleher added a commit to jeromekelleher/tskit that referenced this issue Nov 8, 2021
@mergify mergify bot closed this as completed in bb3c76f Nov 11, 2021
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