biom-format
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biocore
The Biological Observation Matrix (BIOM) Format Project
This table: ``` python > t.metadata() Out[5]: (defaultdict(, {u'pH': 7.0}), defaultdict(, {u'pH': 8.0}), defaultdict(, {u'pH': 7.0}), defaultdict(, {})) ``` Will cause `to_hdf5` to except. It is valid for `to_json`.
...like the [scikit-bio](https://pypi.python.org/pypi/scikit-bio) one
Just like in: https://github.com/biocore/qiime/pull/1657/files#diff-5c0794232d97a5a24529f1e340f1bea5R19
A continuation of PR #949, this PR adds support for Windows. All issues revolve around two things: 1) File path separators differing between operating systems. `/` vs. `\` 2) Temporary...
Hi @wasade I was able to set up a development environment with NumPy 2.0, following the instruction provided in #955 . Now as I run `python -m unittest`, there are...
@rgommers We still got an error even with NumPy 2.0-compatible h5py and Pandas installed. Could you please help? How to reproduce the error: ``` git clone https://github.com/biocore/biom-format.git cd biom-format conda...
This was originally posted on the qiime2 issue tracker https://github.com/qiime2/q2-feature-table/issues/245 I'm able to replicate it with some of my own data, and the results are a bit perplexing. When I...
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...
Hi, I'm considering adding an option to SingleM to allow BIOM format as an output. The problem is that I'm not sure about what the canonical way to do this...
