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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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align_tree cannot handle features with 0 counts #948

Closed dpear closed 3 months ago

dpear commented 4 months ago

if a feature table has a feature with 0 sum, align_tree will throw an error stating that the id of the feature is not present in the table. (apologies for brevity, let me know and I can follow up with code examples etc.)

mortonjt commented 4 months ago

Hi, did you try this workaround : https://github.com/biocore/biom-format/issues/860 As @wasade and I discussed in previous iterations, if we explicitly store zeros in the biom table, it sort of thwarts bioms' ability to have memory efficient storage.

wasade commented 4 months ago

Thanks, @mortonjt! But there is an edge case here that needs to be fixed. sort_order based off the tree, but called after remove_empty which will raise if a feature is removed.

wasade commented 3 months ago

Fixed in #959, unsure why it didn't automatically close.