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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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definition of "empty" biom table differs #582

Closed gregcaporaso closed 7 years ago

gregcaporaso commented 9 years ago

There are two different definitions for "empty" for a Table object.

The first is if a table has all zero values, and the second is if a table has either no sample ids or no observation ids. It's not immediately clear to @jairideout and I which of these is the better definition, but these should be unified.

jairideout commented 9 years ago

:+1:, it looks like the former definition is assumed in QIIME's rarefaction code (see this line and https://github.com/biocore/qiime/issues/1836 for more details), but the BIOM code uses the latter definition.

wasade commented 9 years ago

@gregcaporaso or @jairideout, can I assign either of you this for the pending minor bugfix release?

jairideout commented 9 years ago

I'm not comfortable working on this because I'm not sure how this will affect backwards-compatibility with QIIME or what the correct definition of "empty" is in the context of BIOM. This may be better to define when Table is ported to scikit-bio.

wasade commented 9 years ago

Sounds good, thanks

On Tue, Mar 3, 2015 at 12:08 PM, Jai Ram Rideout notifications@github.com wrote:

I'm not comfortable working on this because I'm not sure how this will affect backwards-compatibility with QIIME or what the correct definition of "empty" is in the context of BIOM. This may be better to define when Table is ported to scikit-bio.

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/582#issuecomment-77012110.

wasade commented 7 years ago

This is actually a documentation issue. The references cited in the seed for this issue are actually consistent in the behavior of the code as err performs its check against Table.is_empty().