biom-format
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biocore
The Biological Observation Matrix (BIOM) Format Project
# Reproducible example Example code based on https://biom-format.org/documentation/table_objects.html#examples ```python import numpy as np from biom.table import Table data = np.arange(40).reshape(10, 4) sample_ids = ["S%d" % i for i in range(4)]...
Exchanging data in the biom format between Python (using the biom-format package) and R (using [rbiom](https://github.com/cmmr/rbiom)) is using different and incompatible formats: * On the Python side, taxonomy is typically...
When trying to add biom-format support for aarch64 conda, I encountered the following error [here](https://github.com/scikit-bio/scikit-bio/actions/runs/7479978639/job/20358363268?pr=1907#step:5:647), which caused the build to fail. The error message I received was _"PackagesNotFoundError: The following...
See https://forum.qiime2.org/t/conversion-of-biom-to-tsv-not-working/28907/9 A consequence of this is conversion to TSV is failing
See https://forum.qiime2.org/t/conversion-of-biom-to-tsv-not-working/28907/9
See https://forum.qiime2.org/t/conversion-of-biom-to-tsv-not-working/28907/9
`update_ids(..., strict=False)` appears to detect duplicate IDs. The issue is not isolated, and a minimal example with the `example_table` did not work on a first attempt.
...to allow for calling `remove_empty` and for removing samples which do not fall into a bin. See https://github.com/qiime2/q2-feature-table/pull/277#discussion_r1277792071 cc @gregcaporaso
See [here](https://cibuildwheel.readthedocs.io/en/stable/options/#test-command)